1 |
gezelter |
2199 |
2005-04-14 16:20 gezelter |
2 |
tim |
2102 |
|
3 |
gezelter |
2199 |
* src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of |
4 |
|
|
MoLocator |
5 |
|
|
|
6 |
|
|
2005-04-14 14:12 gezelter |
7 |
|
|
|
8 |
|
|
* LICENSE: [no log message] |
9 |
|
|
|
10 |
|
|
2005-04-14 11:10 chuckv |
11 |
|
|
|
12 |
|
|
* src/applications/nanoRodBuilder/nanorodBuilder.cpp: |
13 |
|
|
nanorodbuilder now exit's when libCGAL is not present. |
14 |
|
|
|
15 |
|
|
2005-04-14 10:20 tim |
16 |
|
|
|
17 |
|
|
* src/io/make_nodes.h: fix one more warning message in make_nodes |
18 |
|
|
|
19 |
|
|
2005-04-13 18:36 chuckv |
20 |
|
|
|
21 |
|
|
* src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed |
22 |
|
|
interface name for SGI Compiler |
23 |
|
|
|
24 |
|
|
2005-04-13 18:29 chrisfen |
25 |
|
|
|
26 |
|
|
* samples/water/ssde/ssde.md: oops... bad sample |
27 |
|
|
|
28 |
|
|
2005-04-13 18:00 chuckv |
29 |
|
|
|
30 |
|
|
* src/config.h.in: Change typo in CGAL. |
31 |
|
|
|
32 |
|
|
2005-04-13 17:43 tim |
33 |
|
|
|
34 |
|
|
* src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp, |
35 |
|
|
selection/SelectionCompiler.hpp: fix some warning messages |
36 |
|
|
|
37 |
|
|
2005-04-13 17:30 gezelter |
38 |
|
|
|
39 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
40 |
|
|
make/Makefile.in, src/config.h.in, |
41 |
|
|
src/applications/nanoRodBuilder/Makefile, |
42 |
|
|
src/applications/nanoRodBuilder/Makefile.in, |
43 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL |
44 |
|
|
checks |
45 |
|
|
|
46 |
|
|
2005-04-13 15:36 chuckv |
47 |
|
|
|
48 |
|
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp, |
49 |
|
|
DarkSide/LJ.F90, DarkSide/electrostatic.F90, |
50 |
|
|
DarkSide/electrostatic_interface.F90, |
51 |
|
|
DarkSide/electrostatic_interface.h, DarkSide/lj_interface.F90, |
52 |
|
|
DarkSide/lj_interface.h, DarkSide/sticky.F90, |
53 |
|
|
DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added |
54 |
|
|
destroy methods for Fortran modules. |
55 |
|
|
|
56 |
|
|
2005-04-13 15:17 chuckv |
57 |
|
|
|
58 |
|
|
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90, |
59 |
|
|
shapes_interface.h: Added destroy method to clean up memory |
60 |
|
|
|
61 |
|
|
2005-04-13 13:41 tim |
62 |
|
|
|
63 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
64 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
65 |
|
|
io/make_nodes.c, io/parse_tree.c, primitives/Bend.hpp, |
66 |
|
|
primitives/Bond.hpp, primitives/Torsion.hpp, types/MakeStamps.cpp, |
67 |
|
|
types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are |
68 |
|
|
fixed |
69 |
|
|
|
70 |
|
|
2005-04-12 17:44 chuckv |
71 |
|
|
|
72 |
|
|
* src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed |
73 |
|
|
for nanoRodBuilder. |
74 |
|
|
|
75 |
|
|
2005-04-12 17:42 tim |
76 |
|
|
|
77 |
|
|
* src/applications/: nanoRodBuilder/nanorodBuilder.cpp, |
78 |
|
|
simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder |
79 |
|
|
and simpleBuilder(forget to delete lattice) |
80 |
|
|
|
81 |
|
|
2005-04-12 17:33 tim |
82 |
|
|
|
83 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
84 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp: |
85 |
|
|
refactory lattice |
86 |
|
|
|
87 |
|
|
2005-04-12 17:07 tim |
88 |
|
|
|
89 |
|
|
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp, |
90 |
|
|
CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp, |
91 |
|
|
Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory |
92 |
|
|
LatticeFactory and LatticeCreator |
93 |
|
|
|
94 |
|
|
2005-04-12 16:58 tim |
95 |
|
|
|
96 |
|
|
* src/: applications/nanoRodBuilder/nanorodBuilder.cpp, |
97 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp, |
98 |
|
|
brains/Register.hpp, lattice/Lattice.cpp, lattice/Lattice.hpp, |
99 |
|
|
lattice/LatticeCreator.cpp, lattice/LatticeCreator.hpp, |
100 |
|
|
lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp, |
101 |
|
|
lattice/Makefile: refactory LatticeFactory and LatticeCreator |
102 |
|
|
|
103 |
|
|
2005-04-12 16:28 gezelter |
104 |
|
|
|
105 |
|
|
* src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp, |
106 |
|
|
vector_class.F90: cleaned up vector_class memory leak fix by |
107 |
|
|
deallocating in reverse order of how we allocated. Also migrated |
108 |
|
|
MoLocator into utils directory |
109 |
|
|
|
110 |
|
|
2005-04-12 16:27 gezelter |
111 |
|
|
|
112 |
|
|
* src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp, |
113 |
|
|
Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
114 |
|
|
LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice |
115 |
|
|
directory |
116 |
|
|
|
117 |
|
|
2005-04-12 16:27 gezelter |
118 |
|
|
|
119 |
|
|
* src/applications/: nanoRodBuilder/BaseLattice.cpp, |
120 |
|
|
nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp, |
121 |
|
|
nanoRodBuilder/Lattice.hpp, nanoRodBuilder/LatticeCreator.cpp, |
122 |
|
|
nanoRodBuilder/LatticeCreator.hpp, |
123 |
|
|
nanoRodBuilder/LatticeFactory.cpp, |
124 |
|
|
nanoRodBuilder/LatticeFactory.hpp, nanoRodBuilder/Makefile, |
125 |
|
|
nanoRodBuilder/MoLocator.cpp, nanoRodBuilder/MoLocator.hpp, |
126 |
|
|
nanoRodBuilder/nanorodBuilder.cpp, simpleBuilder/BaseLattice.cpp, |
127 |
|
|
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
128 |
|
|
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
129 |
|
|
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
130 |
|
|
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Makefile, |
131 |
|
|
simpleBuilder/MoLocator.cpp, simpleBuilder/MoLocator.hpp, |
132 |
|
|
simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of |
133 |
|
|
these files are now redundant |
134 |
|
|
|
135 |
|
|
2005-04-12 16:27 gezelter |
136 |
|
|
|
137 |
|
|
* src/UseTheForce/DarkSide/: atype_interface.F90, |
138 |
|
|
atype_interface.h: cleaned up memory leak fix |
139 |
|
|
|
140 |
|
|
2005-04-12 16:26 gezelter |
141 |
|
|
|
142 |
|
|
* make/Makefile.in: added lattice subdirectory |
143 |
|
|
|
144 |
|
|
2005-04-12 15:57 chrisfen |
145 |
|
|
|
146 |
|
|
* src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added |
147 |
|
|
a space by accident |
148 |
|
|
|
149 |
|
|
2005-04-12 15:56 chrisfen |
150 |
|
|
|
151 |
|
|
* samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added |
152 |
|
|
quadrupole sample |
153 |
|
|
|
154 |
|
|
2005-04-12 15:56 chrisfen |
155 |
|
|
|
156 |
|
|
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating |
157 |
|
|
samples |
158 |
|
|
|
159 |
|
|
2005-04-12 13:30 tim |
160 |
|
|
|
161 |
|
|
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom |
162 |
|
|
type in fortran side |
163 |
|
|
|
164 |
|
|
2005-04-12 12:45 chuckv |
165 |
|
|
|
166 |
|
|
* src/utils/vector_class.F90: Further changes to vector_class |
167 |
|
|
destroy function. |
168 |
|
|
|
169 |
|
|
2005-04-12 12:39 chuckv |
170 |
|
|
|
171 |
|
|
* src/utils/vector_class.F90: Fixed pointer memory leak in |
172 |
|
|
vector_class. |
173 |
|
|
|
174 |
|
|
2005-04-12 12:12 chuckv |
175 |
|
|
|
176 |
|
|
* src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp, |
177 |
|
|
DarkSide/atype_interface.F90, DarkSide/atype_interface.h, |
178 |
|
|
DarkSide/eam.F90, DarkSide/eam_interface.F90, |
179 |
|
|
DarkSide/eam_interface.h: Updates to deallocate object in fortran. |
180 |
|
|
|
181 |
|
|
2005-04-12 09:24 chrisfen |
182 |
|
|
|
183 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: minor change to TI |
184 |
|
|
output |
185 |
|
|
|
186 |
|
|
2005-04-11 19:29 chuckv |
187 |
|
|
|
188 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
189 |
|
|
applications/nanoRodBuilder/Makefile: Changes to delete atypes... |
190 |
|
|
|
191 |
|
|
2005-04-11 19:28 chuckv |
192 |
|
|
|
193 |
|
|
* src/utils/vector_class.F90: Added code to delete vector. |
194 |
|
|
|
195 |
|
|
2005-04-11 17:03 chuckv |
196 |
|
|
|
197 |
|
|
* samples/metals/nanorod/: Au_nanoparticle.md, |
198 |
|
|
Au_nanoparticle_FCC.md, Au_nanoparticle_linux.md, metals.md: Why |
199 |
|
|
aren't these here? |
200 |
|
|
|
201 |
|
|
2005-04-11 16:58 tim |
202 |
|
|
|
203 |
|
|
* src/io/basic_ifstrstream.hpp: avoid multiple inherit in |
204 |
|
|
basic_ifstrstream |
205 |
|
|
|
206 |
|
|
2005-04-11 16:37 chuckv |
207 |
|
|
|
208 |
|
|
* make/Makefile.in, |
209 |
|
|
src/applications/nanoRodBuilder/BaseLattice.cpp, |
210 |
|
|
src/applications/nanoRodBuilder/BaseLattice.hpp, |
211 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.cpp, |
212 |
|
|
src/applications/nanoRodBuilder/GeometryBuilder.hpp, |
213 |
|
|
src/applications/nanoRodBuilder/Lattice.cpp, |
214 |
|
|
src/applications/nanoRodBuilder/Lattice.hpp, |
215 |
|
|
src/applications/nanoRodBuilder/LatticeCreator.cpp, |
216 |
|
|
src/applications/nanoRodBuilder/LatticeCreator.hpp, |
217 |
|
|
src/applications/nanoRodBuilder/LatticeFactory.cpp, |
218 |
|
|
src/applications/nanoRodBuilder/LatticeFactory.hpp, |
219 |
|
|
src/applications/nanoRodBuilder/Makefile, |
220 |
|
|
src/applications/nanoRodBuilder/MoLocator.cpp, |
221 |
|
|
src/applications/nanoRodBuilder/MoLocator.hpp, |
222 |
|
|
src/applications/nanoRodBuilder/nanoBuilder.ggo, |
223 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.cpp, |
224 |
|
|
src/applications/nanoRodBuilder/nanorodBuilder.ggo, |
225 |
|
|
src/applications/nanoRodBuilder/nanorodBuilderCmd.c, |
226 |
|
|
src/applications/nanoRodBuilder/nanorodBuilderCmd.h: Importing |
227 |
|
|
nanoRodBuilder application (may not work yet). ((Doesn't work |
228 |
|
|
yet.)) (((May never work....))) |
229 |
|
|
|
230 |
|
|
2005-04-11 15:54 tim |
231 |
|
|
|
232 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete |
233 |
|
|
prepareVisitor in Dump2XYZ |
234 |
|
|
|
235 |
|
|
2005-04-11 15:19 chrisfen |
236 |
|
|
|
237 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixing of the |
238 |
|
|
quadrupoles. look! it's divide by 3 like stone says! |
239 |
|
|
|
240 |
|
|
2005-04-11 15:18 chrisfen |
241 |
|
|
|
242 |
|
|
* forceFields/DUFF2.frc: fixing of the quadrupoles |
243 |
|
|
|
244 |
|
|
2005-04-11 15:16 tim |
245 |
|
|
|
246 |
|
|
* src/selection/Token.hpp: change the parameter name in |
247 |
|
|
constructors |
248 |
|
|
|
249 |
|
|
2005-04-11 14:49 gezelter |
250 |
|
|
|
251 |
|
|
* make/Makefile.in: One more bug fix for GNU make versions < 3.80 |
252 |
|
|
|
253 |
|
|
2005-04-11 14:06 gezelter |
254 |
|
|
|
255 |
|
|
* make/Makefile.in: Fixed the uc and lc functions for GNU make |
256 |
|
|
versions < 3.80 |
257 |
|
|
|
258 |
|
|
2005-04-11 11:13 gezelter |
259 |
|
|
|
260 |
|
|
* make/Makefile.in, src/UseTheForce/Makefile, |
261 |
|
|
src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added |
262 |
|
|
some stuff to clean out module files during "make clean" |
263 |
|
|
|
264 |
|
|
2005-04-08 17:13 chrisfen |
265 |
|
|
|
266 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: quadrupole |
267 |
|
|
interactions should be working with a remaining question of |
268 |
|
|
interaction magnitude |
269 |
|
|
|
270 |
|
|
2005-04-08 17:12 chrisfen |
271 |
|
|
|
272 |
|
|
* samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with |
273 |
|
|
samples |
274 |
|
|
|
275 |
|
|
2005-04-08 13:48 chrisfen |
276 |
|
|
|
277 |
|
|
* samples/water/ssd/ssd.md: oops... messed up a sample |
278 |
|
|
|
279 |
|
|
2005-04-08 09:43 chrisfen |
280 |
|
|
|
281 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix |
282 |
|
|
charge-dipole interactions |
283 |
|
|
|
284 |
|
|
2005-04-08 09:42 chrisfen |
285 |
|
|
|
286 |
|
|
* samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md, |
287 |
|
|
ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole |
288 |
|
|
|
289 |
|
|
2005-04-08 09:41 chrisfen |
290 |
|
|
|
291 |
|
|
* forceFields/DUFF2.frc: added Cl- and Na+ |
292 |
|
|
|
293 |
|
|
2005-04-06 18:59 tim |
294 |
|
|
|
295 |
|
|
* src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser |
296 |
|
|
|
297 |
|
|
2005-04-05 18:09 tim |
298 |
|
|
|
299 |
|
|
* src/selection/: NameFinder.cpp, SelectionCompiler.cpp, |
300 |
|
|
SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-' |
301 |
|
|
in atom type name;clean the code a little bit |
302 |
|
|
|
303 |
|
|
2005-03-29 16:00 tim |
304 |
|
|
|
305 |
|
|
* src/math/: ChebyshevPolynomials.cpp, SquareMatrix3.hpp: fix a bug |
306 |
|
|
in converting rotation matrix to quaternion |
307 |
|
|
|
308 |
|
|
2005-03-28 17:41 tim |
309 |
|
|
|
310 |
|
|
* src/visitors/LipidTransVisitor.cpp: fixed the wrapping |
311 |
|
|
|
312 |
|
|
2005-03-28 17:30 tim |
313 |
|
|
|
314 |
|
|
* src/visitors/LipidTransVisitor.cpp: LipidTranVisitor should do |
315 |
|
|
the wrapping |
316 |
|
|
|
317 |
|
|
2005-03-28 10:54 tim |
318 |
|
|
|
319 |
|
|
* src/applications/staticProps/GofXyz.cpp: fix a bug in getting the |
320 |
|
|
dimension of histogram |
321 |
|
|
|
322 |
|
|
2005-03-22 11:38 tim |
323 |
|
|
|
324 |
|
|
* make/Makefile.in, src/applications/dump2Xyz/Makefile, |
325 |
|
|
src/applications/dynamicProps/Makefile, |
326 |
|
|
src/applications/oopse/Makefile, |
327 |
|
|
src/applications/simpleBuilder/Makefile, |
328 |
|
|
src/applications/staticProps/Makefile: avoid building parallel |
329 |
|
|
executable for dump2XYZ, simpleBuilder, staticProps and |
330 |
|
|
dynamicProps |
331 |
|
|
|
332 |
|
|
2005-03-21 17:34 chrisfen |
333 |
|
|
|
334 |
|
|
* forceFields/: DUFF2.frc, WATER.frc: Corrected changes to the |
335 |
|
|
forcefield files |
336 |
|
|
|
337 |
|
|
2005-03-21 15:51 chrisfen |
338 |
|
|
|
339 |
|
|
* src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90, |
340 |
|
|
DarkSide/reactionField.F90: Make sure electrostatic_module provides |
341 |
|
|
data for reaction_field |
342 |
|
|
|
343 |
|
|
2005-03-21 15:50 chrisfen |
344 |
|
|
|
345 |
|
|
* forceFields/: DUFF2.frc, WATER.frc: Chris debugging stuff. HE |
346 |
|
|
WILL CHANGE THIS BACK, RIGHT? |
347 |
|
|
|
348 |
|
|
2005-03-21 14:23 gezelter |
349 |
|
|
|
350 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: constant back to |
351 |
|
|
correct value |
352 |
|
|
|
353 |
|
|
2005-03-21 14:22 gezelter |
354 |
|
|
|
355 |
|
|
* make/Makefile.in: fixed an install-related bug. |
356 |
|
|
$(InstallCommand) had been set to $(InstallData) |
357 |
|
|
|
358 |
|
|
2005-03-15 09:21 gezelter |
359 |
|
|
|
360 |
|
|
* src/integrators/Integrator.cpp: VelocityVerletIntegrator already |
361 |
|
|
deletes and Nullifies restWriter, so Integrator shouldn't do it. |
362 |
|
|
|
363 |
|
|
2005-03-15 09:20 gezelter |
364 |
|
|
|
365 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: fixed three typos |
366 |
|
|
|
367 |
|
|
2005-03-13 02:39 gezelter |
368 |
|
|
|
369 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: first run at |
370 |
|
|
charge-quadrupole interactions |
371 |
|
|
|
372 |
|
|
2005-03-12 14:12 chrisfen |
373 |
|
|
|
374 |
|
|
* samples/: Makefile.in, thermoIntegration/liquid/Makefile, |
375 |
|
|
thermoIntegration/solid/Makefile: forgot a couple of makefiles |
376 |
|
|
|
377 |
|
|
2005-03-12 14:05 chrisfen |
378 |
|
|
|
379 |
|
|
* samples/thermoIntegration/liquid/ssde.in, |
380 |
|
|
samples/thermoIntegration/liquid/ssde.md, |
381 |
|
|
samples/thermoIntegration/liquid/water.md, |
382 |
|
|
samples/thermoIntegration/solid/idealCrystal.in, |
383 |
|
|
samples/thermoIntegration/solid/ssde.in, |
384 |
|
|
samples/thermoIntegration/solid/ssde.md, |
385 |
|
|
samples/thermoIntegration/solid/ssde.zang0, |
386 |
|
|
samples/thermoIntegration/solid/water.md, |
387 |
|
|
samples/water/tip3p_ice/tp3.md, |
388 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
389 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: added some |
390 |
|
|
samples |
391 |
|
|
|
392 |
|
|
2005-03-11 12:50 tim |
393 |
|
|
|
394 |
|
|
* src/: brains/SimCreator.cpp, |
395 |
|
|
io/MultipoleAtomTypesSectionParser.cpp: fix a typo in |
396 |
|
|
MultipoleAtomTypesSectionParser |
397 |
|
|
|
398 |
|
|
2005-03-11 10:55 tim |
399 |
|
|
|
400 |
|
|
* src/brains/SimInfo.cpp: pairs inside cutoff group should not be |
401 |
|
|
excluded |
402 |
|
|
|
403 |
|
|
2005-03-11 10:53 gezelter |
404 |
|
|
|
405 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: settled on a unit for |
406 |
|
|
quadrupoles |
407 |
|
|
|
408 |
|
|
2005-03-11 10:52 gezelter |
409 |
|
|
|
410 |
|
|
* forceFields/DUFF2.frc: quadrupoles for SSD models |
411 |
|
|
|
412 |
|
|
2005-03-11 10:00 tim |
413 |
|
|
|
414 |
|
|
* ChangeLog, doc/SelectionExpression.html, |
415 |
|
|
doc/classoopse_1_1StuntDouble.png, doc/definition.jpg, |
416 |
|
|
doc/gofr.jpg, doc/gofrtheta.jpg, doc/heirarchy.png, |
417 |
|
|
src/brains/SimInfo.cpp, src/selection/SelectionEvaluator.cpp, |
418 |
|
|
src/selection/SelectionEvaluator.hpp, src/selection/Token.hpp, |
419 |
|
|
src/selection/TokenMap.cpp: clean up SimInfo; modify the images of |
420 |
|
|
SelectionExpression.html |
421 |
|
|
|
422 |
|
|
2005-03-10 19:43 chrisfen |
423 |
|
|
|
424 |
tim |
2116 |
* samples/water/ssde/ssde.md, samples/water/tip3p_ice/tp3.md, |
425 |
|
|
src/io/RestReader.cpp, src/restraints/Restraints.cpp, |
426 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixed a bug in |
427 |
|
|
MPI restraints |
428 |
|
|
|
429 |
gezelter |
2199 |
2005-03-10 18:56 tim |
430 |
tim |
2116 |
|
431 |
|
|
* doc/SelectionExpression.html, src/brains/SimInfo.cpp, |
432 |
|
|
src/primitives/CutoffGroup.hpp: adding exclude pairs for rigidbody |
433 |
|
|
and cutoff group |
434 |
|
|
|
435 |
gezelter |
2199 |
2005-03-10 17:06 gezelter |
436 |
tim |
2116 |
|
437 |
|
|
* src/types/MorseBondType.hpp: fixed a doxygen problem |
438 |
|
|
|
439 |
gezelter |
2199 |
2005-03-10 16:51 gezelter |
440 |
tim |
2116 |
|
441 |
|
|
* samples/dipole/: split_SSD.md, twoSplitDipole.md: messing with |
442 |
|
|
the split dipole test cases |
443 |
|
|
|
444 |
gezelter |
2199 |
2005-03-10 16:51 gezelter |
445 |
tim |
2116 |
|
446 |
|
|
* doc/SelectionExpression.html: updated some documentation |
447 |
|
|
|
448 |
gezelter |
2199 |
2005-03-10 15:40 gezelter |
449 |
tim |
2116 |
|
450 |
|
|
* src/io/: Globals.hpp, LinkedCommand.cpp, LinkedCommand.hpp, |
451 |
|
|
Makefile: LinkedList removal project starts now |
452 |
|
|
|
453 |
gezelter |
2199 |
2005-03-10 15:28 tim |
454 |
tim |
2116 |
|
455 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
456 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/Globals.cpp, io/Globals.hpp: |
457 |
|
|
using map to replace link list |
458 |
|
|
|
459 |
gezelter |
2199 |
2005-03-10 14:11 tim |
460 |
tim |
2116 |
|
461 |
|
|
* samples/dipole/: splitInWater.in, splitInWater.md: adding test |
462 |
|
|
case of split dipole |
463 |
|
|
|
464 |
gezelter |
2199 |
2005-03-10 14:10 chrisfen |
465 |
tim |
2116 |
|
466 |
|
|
* samples/water/tip3p_ice/tp3.md, src/io/RestReader.cpp, |
467 |
|
|
src/io/RestWriter.cpp, |
468 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: Oops... MPI now |
469 |
|
|
builds... |
470 |
|
|
|
471 |
gezelter |
2199 |
2005-03-10 13:44 tim |
472 |
tim |
2116 |
|
473 |
|
|
* samples/dipole/: Lipid.frc, splitDipole.md, split_SSD.in, |
474 |
|
|
split_SSD.md, twoSplitDipole.in, twoSplitDipole.md, water.md: |
475 |
|
|
adding test case for split dipole |
476 |
|
|
|
477 |
gezelter |
2199 |
2005-03-10 12:54 gezelter |
478 |
tim |
2116 |
|
479 |
|
|
* src/UseTheForce/DarkSide/electrostatic.F90: added fortran-side |
480 |
|
|
support for split dipoles |
481 |
|
|
|
482 |
gezelter |
2199 |
2005-03-10 11:27 chrisfen |
483 |
tim |
2116 |
|
484 |
|
|
* samples/water/tip3p_ice/tp3.md, |
485 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixes to |
486 |
|
|
restraints |
487 |
|
|
|
488 |
gezelter |
2199 |
2005-03-10 11:15 chrisfen |
489 |
tim |
2116 |
|
490 |
|
|
* samples/water/tip3p_ice/tp3.md, src/UseTheForce/ForceFields.cpp, |
491 |
|
|
src/UseTheForce/ForceFields.hpp, |
492 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp: fixing restraints |
493 |
|
|
|
494 |
gezelter |
2199 |
2005-03-10 11:14 tim |
495 |
tim |
2116 |
|
496 |
|
|
* ChangeLog, doc/SelectionExpression.html, forceFields/DUFF2.frc, |
497 |
|
|
src/io/MultipoleAtomTypesSectionParser.cpp, |
498 |
|
|
src/selection/SelectionEvaluator.cpp: minor change |
499 |
|
|
|
500 |
gezelter |
2199 |
2005-03-10 10:10 chrisfen |
501 |
tim |
2116 |
|
502 |
tim |
2102 |
* make/Makefile.in, samples/water/tip3p_ice/tp3.md, |
503 |
|
|
src/brains/SimCreator.cpp, src/brains/SimInfo.hpp, |
504 |
|
|
src/integrators/Integrator.cpp, src/integrators/Integrator.hpp, |
505 |
|
|
src/integrators/VelocityVerletIntegrator.cpp, |
506 |
|
|
src/integrators/VelocityVerletIntegrator.hpp, |
507 |
|
|
src/io/DumpReader.cpp, src/io/Globals.cpp, src/io/Globals.hpp, |
508 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/RestReader.cpp, |
509 |
|
|
src/io/RestReader.hpp, src/io/RestWriter.cpp, |
510 |
|
|
src/io/RestWriter.hpp, src/io/RestraintReader.cpp, |
511 |
|
|
src/io/RestraintWriter.cpp, src/restraints/Makefile, |
512 |
|
|
src/restraints/Restraints.cpp, src/restraints/Restraints.hpp, |
513 |
|
|
src/restraints/ThermoIntegrationForceManager.cpp, |
514 |
|
|
src/restraints/ThermoIntegrationForceManager.hpp: First commit of |
515 |
|
|
the new restraints code |
516 |
|
|
|
517 |
gezelter |
2199 |
2005-03-09 13:48 tim |
518 |
tim |
2102 |
|
519 |
|
|
* src/selection/: IndexFinder.cpp, IndexFinder.hpp: adding |
520 |
|
|
IndexFinder |
521 |
|
|
|
522 |
gezelter |
2199 |
2005-03-09 13:46 tim |
523 |
tim |
2102 |
|
524 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.ggo, |
525 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
526 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
527 |
|
|
selection/SelectionCompiler.cpp, selection/SelectionEvaluator.cpp: |
528 |
|
|
fix compilation issue |
529 |
|
|
|
530 |
gezelter |
2199 |
2005-03-09 12:58 tim |
531 |
tim |
2102 |
|
532 |
|
|
* forceFields/DUFF2.frc, scripts/filepp, |
533 |
|
|
src/UseTheForce/EAM_FF.cpp, |
534 |
|
|
src/io/MultipoleAtomTypesSectionParser.cpp, |
535 |
|
|
src/io/SectionParser.cpp, test/math/testRandNumGen.cpp: fix a bug |
536 |
|
|
in SectionParser (lineNo is not updated) |
537 |
|
|
|
538 |
gezelter |
2199 |
2005-03-09 12:30 tim |
539 |
tim |
2102 |
|
540 |
|
|
* src/: UseTheForce/DUFF.cpp, applications/dump2Xyz/Dump2XYZ.cpp, |
541 |
|
|
applications/dump2Xyz/Dump2XYZ.ggo, |
542 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
543 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, brains/SimInfo.cpp, |
544 |
|
|
brains/SimInfo.hpp, io/ChargeAtomTypesSectionParser.cpp, |
545 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
546 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
547 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/Makefile, |
548 |
|
|
io/MultipoleAtomTypesSectionParser.cpp, |
549 |
|
|
io/MultipoleAtomTypesSectionParser.hpp, |
550 |
|
|
io/SectionParserManager.cpp, selection/Makefile, |
551 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
552 |
|
|
types/AtomType.cpp, types/DirectionalAtomType.cpp, |
553 |
|
|
visitors/AtomVisitor.cpp, visitors/OtherVisitor.cpp, |
554 |
|
|
visitors/OtherVisitor.hpp: adding IndexFinder which is used to |
555 |
|
|
select the molecules; Seperate ElectrostaticAtomTypesSectionParser |
556 |
|
|
into ChargeAtomTypesSectionParser and |
557 |
|
|
MultipoleAtomTypesSectionParser;remove print dipole option from |
558 |
|
|
Dump2XYZ; |
559 |
|
|
|
560 |
gezelter |
2199 |
2005-03-09 12:28 tim |
561 |
tim |
2102 |
|
562 |
|
|
* forceFields/DUFF2.frc: change the format of DUFF2 |
563 |
|
|
|
564 |
gezelter |
2199 |
2005-03-09 10:44 gezelter |
565 |
tim |
2102 |
|
566 |
|
|
* src/UseTheForce/DarkSide/: electrostatic.F90, |
567 |
|
|
electrostatic_interface.F90, electrostatic_interface.h: new |
568 |
|
|
electrostatic module |
569 |
|
|
|
570 |
gezelter |
2199 |
2005-03-09 09:26 gezelter |
571 |
tim |
2102 |
|
572 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
573 |
|
|
DirectionalAtomType.cpp, DirectionalAtomType.hpp: added splitDipole |
574 |
|
|
and fixed quadrupole stuff |
575 |
|
|
|
576 |
gezelter |
2199 |
2005-03-09 09:25 gezelter |
577 |
tim |
2102 |
|
578 |
|
|
* src/UseTheForce/: DUFF.cpp, EAM_FF.cpp: removed #include lines |
579 |
|
|
for outdated charge and dipole interfaces |
580 |
|
|
|
581 |
gezelter |
2199 |
2005-03-08 16:08 gezelter |
582 |
tim |
2102 |
|
583 |
|
|
* samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md, mix.in, |
584 |
|
|
mix.md, mix2.in, mix2.md, ssd.in, ssd.md: addded a few fun |
585 |
|
|
charge-dipole test cases |
586 |
|
|
|
587 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
588 |
tim |
2102 |
|
589 |
|
|
* src/visitors/: AtomData.hpp, AtomVisitor.cpp, OtherVisitor.cpp, |
590 |
|
|
OtherVisitor.hpp, RigidBodyVisitor.cpp, ZconsVisitor.cpp: fixing a |
591 |
|
|
strange icc8 bug (we think). |
592 |
|
|
|
593 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
594 |
tim |
2102 |
|
595 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp: OOPSE_itoa! |
596 |
|
|
|
597 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
598 |
tim |
2102 |
|
599 |
|
|
* src/types/: AtomType.cpp, DirectionalAtomType.cpp: Electrostatic |
600 |
|
|
Unification Project |
601 |
|
|
|
602 |
gezelter |
2199 |
2005-03-08 16:07 gezelter |
603 |
tim |
2102 |
|
604 |
|
|
* src/io/Globals.cpp: Dunno |
605 |
|
|
|
606 |
gezelter |
2199 |
2005-03-08 16:06 gezelter |
607 |
tim |
2102 |
|
608 |
|
|
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp: Using |
609 |
|
|
OOPSE_itoa and checking a NULL left over from the LinkedList days |
610 |
|
|
|
611 |
gezelter |
2199 |
2005-03-08 16:06 gezelter |
612 |
tim |
2102 |
|
613 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
614 |
|
|
atype_interface.F90, atype_interface.h, charge.F90, |
615 |
|
|
charge_interface.F90, charge_interface.h, dipole.F90, |
616 |
|
|
dipole_interface.F90, dipole_interface.h: electrostatic unification |
617 |
|
|
project fixed an uninitialized variable in Lennard Jones mixing map |
618 |
|
|
|
619 |
gezelter |
2199 |
2005-03-08 16:05 gezelter |
620 |
tim |
2102 |
|
621 |
|
|
* src/UseTheForce/doForces.F90: electrostatic unification project |
622 |
|
|
|
623 |
gezelter |
2199 |
2005-03-08 16:05 gezelter |
624 |
tim |
2102 |
|
625 |
|
|
* samples/water/dimer/: two.md, water.md: making some cool test |
626 |
|
|
cases |
627 |
|
|
|
628 |
gezelter |
2199 |
2005-03-08 16:05 gezelter |
629 |
tim |
2102 |
|
630 |
|
|
* forceFields/DUFF2.frc: Added a charge for Chlorine |
631 |
|
|
|
632 |
gezelter |
2199 |
2005-03-07 17:39 tim |
633 |
tim |
2102 |
|
634 |
|
|
* src/: brains/SimInfo.cpp, io/DumpReader.cpp, |
635 |
|
|
math/ParallelRandNumGen.cpp, math/ParallelRandNumGen.hpp, |
636 |
|
|
primitives/Molecule.cpp, utils/BitSet.cpp, utils/MemoryUtils.hpp: |
637 |
|
|
Fixing a bug in BitSet.cpp |
638 |
|
|
|
639 |
gezelter |
2199 |
2005-03-04 10:28 gezelter |
640 |
tim |
2102 |
|
641 |
|
|
* src/config.h.in: Cleaning up config.h.in by adding comments |
642 |
|
|
|
643 |
gezelter |
2199 |
2005-03-04 10:28 gezelter |
644 |
tim |
2102 |
|
645 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in, |
646 |
|
|
src/brains/SimCreator.cpp: SPRNG eradication project |
647 |
|
|
|
648 |
gezelter |
2199 |
2005-03-03 09:40 tim |
649 |
tim |
2102 |
|
650 |
|
|
* src/io/DumpWriter.cpp: avoid using const char*(hope can fixed the |
651 |
|
|
missing atom type problem) |
652 |
|
|
|
653 |
gezelter |
2199 |
2005-03-02 11:29 tim |
654 |
tim |
2102 |
|
655 |
|
|
* src/math/RandNumGen.hpp: adding base class of Random Number |
656 |
|
|
generator |
657 |
|
|
|
658 |
gezelter |
2199 |
2005-03-02 11:28 tim |
659 |
tim |
2102 |
|
660 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
661 |
|
|
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.hpp: info_ in |
662 |
|
|
Velocitizer is not initialized which causes a seg fault |
663 |
|
|
|
664 |
gezelter |
2199 |
2005-03-02 10:36 tim |
665 |
tim |
2102 |
|
666 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
667 |
|
|
integrators/Velocitizer.hpp, math/Makefile, |
668 |
|
|
math/MersenneTwister.hpp, math/ParallelRandNumGen.cpp, |
669 |
|
|
math/ParallelRandNumGen.hpp, math/SeqRandNumGen.cpp, |
670 |
|
|
math/SeqRandNumGen.hpp: remove default parameter from |
671 |
|
|
MersenneTwister.hpp which causes all kinds of trouble. Refactory |
672 |
|
|
random number generator |
673 |
|
|
|
674 |
gezelter |
2199 |
2005-03-02 02:32 tim |
675 |
tim |
2102 |
|
676 |
|
|
* test/math/testRandNumGen.cpp: Adding unit test for random number |
677 |
|
|
generator |
678 |
|
|
|
679 |
gezelter |
2199 |
2005-03-01 18:17 tim |
680 |
tim |
2102 |
|
681 |
|
|
* src/brains/Thermo.hpp: fixed a file inclusion problem |
682 |
|
|
|
683 |
gezelter |
2199 |
2005-03-01 18:17 tim |
684 |
tim |
2102 |
|
685 |
|
|
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
686 |
|
|
OOPSERandNumGenTestCase.hpp, ParallelandNumGenTestCase.cpp, |
687 |
|
|
ParallelandNumGenTestCase.hpp, RandNumGenTestCase.cpp, |
688 |
|
|
RandNumGenTestCase.hpp: fixed compilation problem |
689 |
|
|
|
690 |
gezelter |
2199 |
2005-03-01 18:02 tim |
691 |
tim |
2102 |
|
692 |
|
|
* src/: brains/SimCreator.cpp, integrators/Velocitizer.cpp, |
693 |
|
|
integrators/Velocitizer.hpp, math/Makefile, |
694 |
|
|
math/OOPSERandNumGen.hpp, math/ParallelRandNumGen.cpp, |
695 |
|
|
math/ParallelRandNumGen.hpp, math/mt19937ar.c, |
696 |
|
|
math/randomSPRNG.cpp, math/randomSPRNG.hpp: replace SPRNG by MTRand |
697 |
|
|
|
698 |
gezelter |
2199 |
2005-03-01 18:00 tim |
699 |
tim |
2102 |
|
700 |
|
|
* test/math/: Makefile, ParallelandNumGenTestCase.cpp, |
701 |
|
|
ParallelandNumGenTestCase.hpp: Change the name of test case |
702 |
|
|
|
703 |
gezelter |
2199 |
2005-03-01 16:00 tim |
704 |
tim |
2102 |
|
705 |
|
|
* test/math/: Makefile, OOPSERandNumGenTestCase.cpp, |
706 |
|
|
OOPSERandNumGenTestCase.hpp: adding testcase for random number |
707 |
|
|
generator |
708 |
|
|
|
709 |
gezelter |
2199 |
2005-03-01 15:10 tim |
710 |
tim |
2102 |
|
711 |
|
|
* src/: UseTheForce/ForceFieldCreator.hpp, brains/SimCreator.hpp, |
712 |
|
|
integrators/IntegratorCreator.hpp, math/MersenneTwister.hpp, |
713 |
|
|
math/Polynomial.hpp, math/Quaternion.hpp, math/RectMatrix.hpp, |
714 |
|
|
math/SquareMatrix.hpp, math/SquareMatrix3.hpp, math/Vector.hpp, |
715 |
|
|
math/Vector3.hpp, minimizers/MinimizerCreator.hpp, |
716 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/GenericData.hpp, |
717 |
|
|
utils/TypeContainer.hpp, visitors/AtomVisitor.cpp, |
718 |
|
|
visitors/RigidBodyVisitor.cpp: fix compilation problem for g++ 3.4 |
719 |
|
|
|
720 |
gezelter |
2199 |
2005-03-01 14:11 tim |
721 |
tim |
2102 |
|
722 |
|
|
* src/: brains/SimCreator.cpp, brains/SimInfo.hpp, |
723 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
724 |
|
|
math/MersenneTwister.hpp, math/OOPSERandNumGen.hpp: adding |
725 |
|
|
OOPSERandNumGen |
726 |
|
|
|
727 |
gezelter |
2199 |
2005-03-01 10:44 gezelter |
728 |
tim |
2102 |
|
729 |
|
|
* make/Makefile.in: Fixed the damned build problem with the |
730 |
|
|
libraries not being removed in make clean and make distclean (at |
731 |
|
|
least we think it is fixed). |
732 |
|
|
|
733 |
gezelter |
2199 |
2005-03-01 10:26 gezelter |
734 |
tim |
2102 |
|
735 |
|
|
* src/math/MersenneTwister.hpp: Making small modifications to allow |
736 |
|
|
for use on MPI machines |
737 |
|
|
|
738 |
gezelter |
2199 |
2005-03-01 09:45 tim |
739 |
tim |
2102 |
|
740 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/SimCreator.cpp, |
741 |
|
|
integrators/Velocitizer.cpp, io/DumpReader.cpp, |
742 |
|
|
math/MersenneTwister.hpp: adding MersenneTwister random number |
743 |
|
|
generator |
744 |
|
|
|
745 |
gezelter |
2199 |
2005-02-28 22:55 tim |
746 |
tim |
2102 |
|
747 |
|
|
* src/math/MersenneTwister.hpp: Adding a modified version of |
748 |
|
|
MersenneTwister.hpp |
749 |
|
|
|
750 |
gezelter |
2199 |
2005-02-28 12:24 tim |
751 |
tim |
2102 |
|
752 |
|
|
* doc/: SelectionExpression.html, classoopse_1_1StuntDouble.png, |
753 |
|
|
definition.jpg: selection expression |
754 |
|
|
|
755 |
gezelter |
2199 |
2005-02-25 16:22 tim |
756 |
tim |
2102 |
|
757 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, |
758 |
|
|
UseTheForce/DarkSide/lj_interface.F90, |
759 |
|
|
UseTheForce/DarkSide/lj_interface.h, |
760 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, types/AtomType.cpp, |
761 |
|
|
types/AtomType.hpp: adding soft potential to LJ Module |
762 |
|
|
|
763 |
gezelter |
2199 |
2005-02-25 11:38 tim |
764 |
tim |
2102 |
|
765 |
|
|
* doc/SelectionExpression.html: adding documentation for selection |
766 |
|
|
expression |
767 |
|
|
|
768 |
gezelter |
2199 |
2005-02-24 15:55 tim |
769 |
tim |
2102 |
|
770 |
|
|
* src/: applications/simpleBuilder/simpleBuilder.cpp, |
771 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/DumpWriter.cpp, |
772 |
|
|
io/DumpWriter.hpp, io/basic_teebuf.hpp, minimizers/Minimizer.cpp: |
773 |
|
|
adding basic_teebuf which can operate on multiple stream |
774 |
|
|
simutaneously. |
775 |
|
|
|
776 |
gezelter |
2199 |
2005-02-22 14:26 chrisfen |
777 |
tim |
2102 |
|
778 |
gezelter |
2199 |
* samples/water/ssdrf/: ssdrf.in, ssdrf.md, water.md: Added ssdrf |
779 |
|
|
sample |
780 |
|
|
|
781 |
|
|
2005-02-22 13:56 tim |
782 |
|
|
|
783 |
tim |
2102 |
* src/: UseTheForce/DarkSide/reactionField.F90, |
784 |
|
|
primitives/RigidBody.cpp: reactionfield get fixed |
785 |
|
|
|
786 |
gezelter |
2199 |
2005-02-21 11:57 tim |
787 |
tim |
2102 |
|
788 |
|
|
* src/: applications/staticProps/GofRAngle.cpp, |
789 |
|
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp: Fix |
790 |
|
|
a bug in GofRAngle |
791 |
|
|
|
792 |
gezelter |
2199 |
2005-02-21 10:28 tim |
793 |
tim |
2102 |
|
794 |
|
|
* src/primitives/Molecule.cpp: Fix for compilation on the Sun |
795 |
|
|
|
796 |
gezelter |
2199 |
2005-02-21 10:22 tim |
797 |
tim |
2102 |
|
798 |
|
|
* src/utils/next_combination.hpp: fix for compilation on the Sun |
799 |
|
|
|
800 |
gezelter |
2199 |
2005-02-21 10:21 tim |
801 |
tim |
2102 |
|
802 |
|
|
* src/utils/GenericData.hpp: fix problem in sun |
803 |
|
|
|
804 |
gezelter |
2199 |
2005-02-18 18:07 tim |
805 |
tim |
2102 |
|
806 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
807 |
|
|
applications/dump2Xyz/Dump2XYZ.ggo, |
808 |
|
|
applications/dump2Xyz/Dump2XYZCmd.c, |
809 |
|
|
applications/dump2Xyz/Dump2XYZCmd.h, |
810 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
811 |
|
|
applications/staticProps/GofXyz.cpp, |
812 |
|
|
applications/staticProps/GofXyz.hpp, |
813 |
|
|
applications/staticProps/StaticProps.cpp, |
814 |
|
|
applications/staticProps/StaticProps.ggo, |
815 |
|
|
applications/staticProps/StaticPropsCmd.c, |
816 |
|
|
applications/staticProps/StaticPropsCmd.h, |
817 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
818 |
|
|
visitors/LipidTransVisitor.cpp, visitors/LipidTransVisitor.hpp, |
819 |
|
|
visitors/Makefile: adding LipidTransVisitor, GofXyz is working now |
820 |
|
|
|
821 |
gezelter |
2199 |
2005-02-18 10:58 gezelter |
822 |
tim |
2102 |
|
823 |
|
|
* src/brains/Register.cpp: Corrected filename collision for EAM on |
824 |
|
|
Mac OS X |
825 |
|
|
|
826 |
gezelter |
2199 |
2005-02-18 10:58 gezelter |
827 |
tim |
2102 |
|
828 |
|
|
* src/applications/oopse/oopse.cpp: Updated copyright information |
829 |
|
|
|
830 |
gezelter |
2199 |
2005-02-18 10:58 gezelter |
831 |
tim |
2102 |
|
832 |
|
|
* src/UseTheForce/: EAM.cpp, EAM.hpp, EAM_FF.cpp, EAM_FF.hpp, |
833 |
|
|
Makefile: corrected filename collision for EAM on operating systems |
834 |
|
|
which are not case sensitive (aka Mac OS X) |
835 |
|
|
|
836 |
gezelter |
2199 |
2005-02-17 15:15 tim |
837 |
tim |
2102 |
|
838 |
|
|
* src/applications/staticProps/GofXyz.cpp: more bug get fixed |
839 |
|
|
|
840 |
gezelter |
2199 |
2005-02-17 14:50 tim |
841 |
tim |
2102 |
|
842 |
|
|
* src/applications/staticProps/: GofXyz.cpp, GofXyz.hpp: fix a bug |
843 |
|
|
in GofXyz |
844 |
|
|
|
845 |
gezelter |
2199 |
2005-02-17 14:09 tim |
846 |
tim |
2102 |
|
847 |
|
|
* src/applications/staticProps/RadialDistrFunc.hpp: make |
848 |
|
|
processHistogram non-abstrct function |
849 |
|
|
|
850 |
gezelter |
2199 |
2005-02-17 13:41 tim |
851 |
tim |
2102 |
|
852 |
|
|
* src/applications/staticProps/GofXyz.cpp: [no log message] |
853 |
|
|
|
854 |
gezelter |
2199 |
2005-02-17 13:30 tim |
855 |
tim |
2102 |
|
856 |
|
|
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
857 |
|
|
GofXyz.cpp, GofXyz.hpp, RadialDistrFunc.cpp, RadialDistrFunc.hpp: |
858 |
|
|
finish GofXyz |
859 |
|
|
|
860 |
gezelter |
2199 |
2005-02-17 11:21 tim |
861 |
tim |
2102 |
|
862 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofR.cpp, |
863 |
|
|
GofRAngle.cpp, GofXyz.cpp: change the output format of 2D radial |
864 |
|
|
distribution function |
865 |
|
|
|
866 |
gezelter |
2199 |
2005-02-17 10:23 tim |
867 |
tim |
2102 |
|
868 |
|
|
* src/utils/BitSet.hpp: forget the const correctness for BitSet |
869 |
|
|
|
870 |
gezelter |
2199 |
2005-02-17 10:18 tim |
871 |
tim |
2102 |
|
872 |
|
|
* src/: brains/BlockSnapshotManager.cpp, |
873 |
|
|
selection/DistanceFinder.cpp: The change of interface of BitSet |
874 |
|
|
cause a bug in SelectionEvaluation |
875 |
|
|
|
876 |
gezelter |
2199 |
2005-02-16 16:13 tim |
877 |
tim |
2102 |
|
878 |
|
|
* src/utils/residentMem.c: return residentMem in byte |
879 |
|
|
|
880 |
gezelter |
2199 |
2005-02-16 16:00 tim |
881 |
tim |
2102 |
|
882 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofRAngle.cpp: fix |
883 |
|
|
a bug in writing out the value of cosang |
884 |
|
|
|
885 |
gezelter |
2199 |
2005-02-16 15:43 tim |
886 |
tim |
2102 |
|
887 |
|
|
* src/brains/BlockSnapshotManager.cpp: using PhysMem - RSSMem to |
888 |
|
|
estimate avaliable memory |
889 |
|
|
|
890 |
gezelter |
2199 |
2005-02-16 15:30 tim |
891 |
tim |
2102 |
|
892 |
|
|
* src/: applications/staticProps/GofAngle2.cpp, |
893 |
|
|
applications/staticProps/GofAngle2.hpp, |
894 |
|
|
applications/staticProps/GofR.cpp, |
895 |
|
|
applications/staticProps/GofR.hpp, |
896 |
|
|
applications/staticProps/GofRAngle.cpp, |
897 |
|
|
applications/staticProps/GofRAngle.hpp, |
898 |
|
|
applications/staticProps/GofXyz.cpp, |
899 |
|
|
applications/staticProps/GofXyz.hpp, |
900 |
|
|
applications/staticProps/StaticProps.cpp, |
901 |
|
|
applications/staticProps/StaticProps.ggo, |
902 |
|
|
applications/staticProps/StaticPropsCmd.c, |
903 |
|
|
applications/staticProps/StaticPropsCmd.h, |
904 |
|
|
brains/BlockSnapshotManager.cpp: change the default bin number |
905 |
|
|
|
906 |
gezelter |
2199 |
2005-02-16 14:36 tim |
907 |
tim |
2102 |
|
908 |
|
|
* src/: applications/dynamicProps/DipoleCorrFunc.cpp, |
909 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
910 |
|
|
applications/dynamicProps/TimeCorrFunc.cpp, |
911 |
|
|
applications/dynamicProps/VCorrFunc.cpp, |
912 |
|
|
applications/staticProps/GofAngle2.cpp, |
913 |
|
|
applications/staticProps/GofR.cpp, |
914 |
|
|
applications/staticProps/GofR.hpp, |
915 |
|
|
applications/staticProps/GofRAngle.cpp, |
916 |
|
|
applications/staticProps/GofRAngle.hpp, |
917 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
918 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
919 |
|
|
selection/SelectionManager.cpp, selection/SelectionManager.hpp, |
920 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp: change the suffix of output |
921 |
|
|
files;fix the problem of counting in staticProps |
922 |
|
|
|
923 |
gezelter |
2199 |
2005-02-15 14:39 tim |
924 |
tim |
2102 |
|
925 |
|
|
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
926 |
|
|
BlockSnapshotManager |
927 |
|
|
|
928 |
gezelter |
2199 |
2005-02-15 14:36 tim |
929 |
tim |
2102 |
|
930 |
|
|
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
931 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
932 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
933 |
|
|
selection/SelectionEvaluator.cpp: BlockSnapshotManager is using |
934 |
|
|
reference counting now |
935 |
|
|
|
936 |
gezelter |
2199 |
2005-02-15 12:49 tim |
937 |
tim |
2102 |
|
938 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
939 |
|
|
replace std::make_pair by VariablesType::value_type to make Sun |
940 |
|
|
Compiler happy |
941 |
|
|
|
942 |
gezelter |
2199 |
2005-02-15 12:35 tim |
943 |
tim |
2102 |
|
944 |
|
|
* src/selection/: TokenMap.cpp, TokenMap.hpp: adding typedef to |
945 |
|
|
TokenMap, using TokenMapType::value_type instead of std::make_pair |
946 |
|
|
to make Sun compiler happy |
947 |
|
|
|
948 |
gezelter |
2199 |
2005-02-15 12:24 tim |
949 |
tim |
2102 |
|
950 |
|
|
* src/applications/staticProps/: GofRAngle.cpp, |
951 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: bug fix in StaticProps |
952 |
|
|
|
953 |
gezelter |
2199 |
2005-02-15 12:11 tim |
954 |
tim |
2102 |
|
955 |
|
|
* src/: applications/staticProps/GofR.cpp, |
956 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
957 |
|
|
applications/staticProps/RadialDistrFunc.hpp, |
958 |
|
|
brains/BlockSnapshotManager.cpp, utils/BitSet.cpp: (1) adding |
959 |
|
|
#ifdef __RWSTD to make sun compiler happy (2) fix pair density |
960 |
|
|
calculation problem when two selections intersect with each other |
961 |
|
|
|
962 |
gezelter |
2199 |
2005-02-15 10:24 gezelter |
963 |
tim |
2102 |
|
964 |
|
|
* src/brains/BlockSnapshotManager.cpp: cast of NULL to satisfy |
965 |
|
|
xlc++ |
966 |
|
|
|
967 |
gezelter |
2199 |
2005-02-15 10:17 gezelter |
968 |
tim |
2102 |
|
969 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
970 |
|
|
src/utils/residentMem.c: [no log message] |
971 |
|
|
|
972 |
gezelter |
2199 |
2005-02-15 01:17 gezelter |
973 |
tim |
2102 |
|
974 |
|
|
* src/utils/residentMem.c: bug fix for null termination |
975 |
|
|
|
976 |
gezelter |
2199 |
2005-02-15 01:11 gezelter |
977 |
tim |
2102 |
|
978 |
|
|
* configure, ac-tools/configure.in, src/utils/residentMem.c: |
979 |
|
|
bugfixing residentMem |
980 |
|
|
|
981 |
gezelter |
2199 |
2005-02-15 00:59 gezelter |
982 |
tim |
2102 |
|
983 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
984 |
|
|
src/utils/residentMem.c: bugfixes for residentMem on LINUX |
985 |
|
|
|
986 |
gezelter |
2199 |
2005-02-15 00:08 gezelter |
987 |
tim |
2102 |
|
988 |
|
|
* src/utils/Makefile.in: added residentMem |
989 |
|
|
|
990 |
gezelter |
2199 |
2005-02-15 00:05 gezelter |
991 |
tim |
2102 |
|
992 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in, |
993 |
|
|
src/config.h.in, src/utils/physmem.h, src/utils/residentMem.c, |
994 |
|
|
src/utils/residentMem.h: modifications to estimate memory in use by |
995 |
|
|
other processes autoconf fixes ps syntax checking config.h file |
996 |
|
|
cleaning |
997 |
|
|
|
998 |
gezelter |
2199 |
2005-02-14 18:26 gezelter |
999 |
tim |
2102 |
|
1000 |
|
|
* configure, ac-tools/configure.in, make/Makefile.in: ps niceness |
1001 |
|
|
|
1002 |
gezelter |
2199 |
2005-02-14 18:16 gezelter |
1003 |
tim |
2102 |
|
1004 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in: ps |
1005 |
|
|
strangeness |
1006 |
|
|
|
1007 |
gezelter |
2199 |
2005-02-14 14:42 tim |
1008 |
tim |
2102 |
|
1009 |
|
|
* src/brains/BlockSnapshotManager.cpp: fix a bug in |
1010 |
|
|
BlockSnapshotManager.hpp |
1011 |
|
|
|
1012 |
gezelter |
2199 |
2005-02-14 13:51 tim |
1013 |
tim |
2102 |
|
1014 |
|
|
* src/applications/staticProps/: StaticProps.cpp, StaticProps.ggo, |
1015 |
|
|
StaticPropsCmd.c: default length for staticProps is 1/2 smallest |
1016 |
|
|
length of first frame |
1017 |
|
|
|
1018 |
gezelter |
2199 |
2005-02-14 13:12 tim |
1019 |
tim |
2102 |
|
1020 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: fix a bug in |
1021 |
|
|
VelocityVerletIntegrator : last frame is written twice |
1022 |
|
|
|
1023 |
gezelter |
2199 |
2005-02-14 12:57 tim |
1024 |
tim |
2102 |
|
1025 |
|
|
* src/: applications/dynamicProps/TimeCorrFunc.cpp, |
1026 |
|
|
brains/SimInfo.cpp, primitives/RigidBody.cpp, |
1027 |
|
|
primitives/StuntDouble.hpp: begin bug fix |
1028 |
|
|
|
1029 |
gezelter |
2199 |
2005-02-14 12:35 tim |
1030 |
tim |
2102 |
|
1031 |
|
|
* src/applications/dynamicProps/: CorrelationFunction.cpp, |
1032 |
|
|
CorrelationFunction.hpp, CrossTimeCorrFunc.cpp, |
1033 |
|
|
CrossTimeCorrFunc.hpp, DipoleCorrFunc.cpp, DipoleCorrFunc.hpp, |
1034 |
|
|
DynamicProps.cpp, FrameTimeCorrFunc.hpp, Makefile, |
1035 |
|
|
ParticleTimeCorrFunc.cpp, ParticleTimeCorrFunc.hpp, RCorrFunc.cpp, |
1036 |
|
|
RCorrFunc.hpp, TimeCorrFunc.cpp, TimeCorrFunc.hpp, VCorrFunc.cpp, |
1037 |
|
|
VCorrFunc.hpp: refactory CorrelationFunction |
1038 |
|
|
|
1039 |
gezelter |
2199 |
2005-02-14 10:18 gezelter |
1040 |
tim |
2102 |
|
1041 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: bug fix |
1042 |
|
|
and start of switch for type of correlation function |
1043 |
|
|
|
1044 |
gezelter |
2199 |
2005-02-13 16:18 tim |
1045 |
tim |
2102 |
|
1046 |
|
|
* src/brains/: DataStorage.cpp, SimInfo.cpp: fix a bug in |
1047 |
|
|
calculating bytes per stuntdouble |
1048 |
|
|
|
1049 |
gezelter |
2199 |
2005-02-13 16:03 tim |
1050 |
tim |
2102 |
|
1051 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: more fix |
1052 |
|
|
|
1053 |
gezelter |
2199 |
2005-02-13 15:57 tim |
1054 |
tim |
2102 |
|
1055 |
|
|
* src/applications/dynamicProps/CorrelationFunction.cpp: fixed a |
1056 |
|
|
bug in CorrelationFunction |
1057 |
|
|
|
1058 |
gezelter |
2199 |
2005-02-13 15:36 tim |
1059 |
tim |
2102 |
|
1060 |
|
|
* src/: applications/staticProps/GofR.cpp, |
1061 |
|
|
applications/staticProps/GofRAngle.cpp, brains/SimInfo.cpp: fixed a |
1062 |
|
|
bug in SimInfo::getCutoff() |
1063 |
|
|
|
1064 |
gezelter |
2199 |
2005-02-13 15:08 tim |
1065 |
tim |
2102 |
|
1066 |
|
|
* make/Makefile.in: adding staticProps and dynamicProps into |
1067 |
|
|
Makefile.in |
1068 |
|
|
|
1069 |
gezelter |
2199 |
2005-02-13 15:05 tim |
1070 |
tim |
2102 |
|
1071 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
1072 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
1073 |
|
|
applications/staticProps/StaticProps.cpp, |
1074 |
|
|
applications/staticProps/StaticProps.ggo, |
1075 |
|
|
applications/staticProps/StaticPropsCmd.c, |
1076 |
|
|
applications/staticProps/StaticPropsCmd.h, brains/SimInfo.cpp, |
1077 |
|
|
brains/SimInfo.hpp, integrators/Integrator.cpp: maximum length |
1078 |
|
|
defaults to the cutoff radius |
1079 |
|
|
|
1080 |
gezelter |
2199 |
2005-02-13 14:14 tim |
1081 |
tim |
2102 |
|
1082 |
|
|
* src/utils/Algorithm.hpp: adding Algorithm.hpp |
1083 |
|
|
|
1084 |
gezelter |
2199 |
2005-02-13 14:10 tim |
1085 |
tim |
2102 |
|
1086 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
1087 |
|
|
applications/dynamicProps/CorrelationFunction.cpp, |
1088 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
1089 |
|
|
applications/dynamicProps/DynamicProps.cpp, |
1090 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
1091 |
|
|
integrators/Integrator.cpp, integrators/Integrator.hpp, |
1092 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
1093 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.cpp, |
1094 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, minimizers/PRCG.cpp, |
1095 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp, utils/physmem.h, |
1096 |
|
|
visitors/OtherVisitor.cpp: dynamicProps get built |
1097 |
|
|
|
1098 |
gezelter |
2199 |
2005-02-13 10:56 tim |
1099 |
tim |
2102 |
|
1100 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
1101 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
1102 |
|
|
brains/DataStorage.cpp, brains/DataStorage.hpp: dynamicProps in |
1103 |
|
|
progress |
1104 |
|
|
|
1105 |
gezelter |
2199 |
2005-02-13 03:04 tim |
1106 |
tim |
2102 |
|
1107 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.hpp, |
1108 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
1109 |
|
|
brains/Makefile, brains/SimInfo.hpp, brains/SimSnapshotManager.cpp, |
1110 |
|
|
brains/SimSnapshotManager.hpp, brains/SnapshotManager.hpp: more |
1111 |
|
|
work in dynamicProps |
1112 |
|
|
|
1113 |
gezelter |
2199 |
2005-02-13 02:25 tim |
1114 |
tim |
2102 |
|
1115 |
|
|
* src/applications/dynamicProps/DynamicProps.cpp: adding |
1116 |
|
|
dynamicProps |
1117 |
|
|
|
1118 |
gezelter |
2199 |
2005-02-13 02:14 tim |
1119 |
tim |
2102 |
|
1120 |
|
|
* src/applications/dynamicProps/: DynamicPropsCmd.c, |
1121 |
|
|
DynamicPropsCmd.h: adding command line option to DynamicProps |
1122 |
|
|
|
1123 |
gezelter |
2199 |
2005-02-13 02:13 tim |
1124 |
tim |
2102 |
|
1125 |
|
|
* src/applications/dynamicProps/: DynamicProps.ggo, Makefile: |
1126 |
|
|
adding command line option for DynamicProps |
1127 |
|
|
|
1128 |
gezelter |
2199 |
2005-02-13 01:57 tim |
1129 |
tim |
2102 |
|
1130 |
|
|
* src/: applications/dynamicProps/CorrelationFunction.cpp, |
1131 |
|
|
applications/dynamicProps/CorrelationFunction.hpp, |
1132 |
|
|
applications/dynamicProps/DipoleCorrFunc.cpp, |
1133 |
|
|
applications/dynamicProps/DipoleCorrFunc.hpp, |
1134 |
|
|
applications/dynamicProps/RCorrFunc.cpp, |
1135 |
|
|
applications/dynamicProps/RCorrFunc.hpp, |
1136 |
|
|
applications/dynamicProps/VCorrFunc.cpp, |
1137 |
|
|
applications/dynamicProps/VCorrFunc.hpp, |
1138 |
|
|
applications/staticProps/RadialDistrFunc.cpp, |
1139 |
|
|
brains/BlockSnapshotManager.cpp, brains/BlockSnapshotManager.hpp, |
1140 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
1141 |
|
|
brains/SnapshotManager.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
1142 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp: adding |
1143 |
|
|
dynamicProps |
1144 |
|
|
|
1145 |
gezelter |
2199 |
2005-02-12 15:09 tim |
1146 |
tim |
2102 |
|
1147 |
|
|
* src/selection/SelectionManager.cpp: adding SelectionManager.cpp |
1148 |
|
|
|
1149 |
gezelter |
2199 |
2005-02-11 17:41 tim |
1150 |
tim |
2102 |
|
1151 |
|
|
* src/brains/: SimInfo.cpp, SimInfo.hpp, Snapshot.hpp: adding one |
1152 |
|
|
more constructor to Snapshot to create customized DataStorage |
1153 |
|
|
|
1154 |
gezelter |
2199 |
2005-02-11 17:39 tim |
1155 |
tim |
2102 |
|
1156 |
|
|
* src/selection/: DistanceFinder.hpp, Makefile, |
1157 |
|
|
SelectionManager.hpp: adding beginSelected, nextSelected method to |
1158 |
|
|
SelectionManager |
1159 |
|
|
|
1160 |
gezelter |
2199 |
2005-02-11 17:36 tim |
1161 |
tim |
2102 |
|
1162 |
|
|
* src/config.h.in, configure: adding support for physmem |
1163 |
|
|
|
1164 |
gezelter |
2199 |
2005-02-11 17:35 tim |
1165 |
tim |
2102 |
|
1166 |
|
|
* ac-tools/configure.in: adding supprot for physmem |
1167 |
|
|
|
1168 |
gezelter |
2199 |
2005-02-11 17:35 tim |
1169 |
tim |
2102 |
|
1170 |
|
|
* src/utils/: BitSet.hpp, Makefile.in, physmem.c, physmem.h: adding |
1171 |
|
|
physmem |
1172 |
|
|
|
1173 |
gezelter |
2199 |
2005-02-10 17:37 tim |
1174 |
tim |
2102 |
|
1175 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
1176 |
|
|
GofR.cpp, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, GofXyz.cpp, |
1177 |
|
|
GofXyz.hpp, Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
1178 |
|
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
1179 |
|
|
StaticPropsCmd.h: more work in StaticProps |
1180 |
|
|
|
1181 |
gezelter |
2199 |
2005-02-10 13:14 tim |
1182 |
tim |
2102 |
|
1183 |
|
|
* src/applications/staticProps/: GofAngle2.cpp, GofAngle2.hpp, |
1184 |
|
|
GofR.cpp, GofR.ggo, GofR.hpp, GofRAngle.cpp, GofRAngle.hpp, |
1185 |
|
|
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofXyz.cpp, GofXyz.hpp, |
1186 |
|
|
Makefile, RadialDistrFunc.cpp, RadialDistrFunc.hpp, |
1187 |
|
|
StaticProps.cpp, StaticProps.ggo, StaticPropsCmd.c, |
1188 |
|
|
StaticPropsCmd.h: change the filenames |
1189 |
|
|
|
1190 |
gezelter |
2199 |
2005-02-10 09:15 tim |
1191 |
tim |
2102 |
|
1192 |
|
|
* src/applications/staticProps/: GofR.cpp, GofRAngle.cpp, |
1193 |
|
|
GofRAngle.hpp, GofRMain.cpp, RadialDistrFunc.cpp, |
1194 |
|
|
RadialDistrFunc.hpp: adding GofRAngle |
1195 |
|
|
|
1196 |
gezelter |
2199 |
2005-02-09 13:21 tim |
1197 |
tim |
2102 |
|
1198 |
|
|
* src/applications/staticProps/: GofrCmd.c, GofrCmd.h: remove some |
1199 |
|
|
useless files |
1200 |
|
|
|
1201 |
gezelter |
2199 |
2005-02-09 13:12 tim |
1202 |
tim |
2102 |
|
1203 |
|
|
* src/applications/staticProps/: GofR.cpp, Makefile, |
1204 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: staticProps in progress |
1205 |
|
|
|
1206 |
gezelter |
2199 |
2005-02-09 12:08 tim |
1207 |
tim |
2102 |
|
1208 |
|
|
* src/applications/staticProps/: GofR.cpp, GofR.ggo, GofR.hpp, |
1209 |
|
|
GofRCmd.c, GofRCmd.h, GofRMain.cpp, GofrCmd.c, GofrCmd.h, |
1210 |
|
|
RadialDistrFunc.cpp, RadialDistrFunc.hpp: adding GofR |
1211 |
|
|
|
1212 |
gezelter |
2199 |
2005-02-07 17:39 tim |
1213 |
tim |
2102 |
|
1214 |
|
|
* src/primitives/Molecule.hpp: add getRigidBodyAt function into |
1215 |
|
|
Molecule class |
1216 |
|
|
|
1217 |
gezelter |
2199 |
2005-02-07 17:38 tim |
1218 |
tim |
2102 |
|
1219 |
|
|
* src/applications/dump2Xyz/Dump2XYZCmd.c: update help info |
1220 |
|
|
|
1221 |
gezelter |
2199 |
2005-02-07 17:36 tim |
1222 |
tim |
2102 |
|
1223 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
1224 |
|
|
SelectionCompiler.cpp: support select internal index selection, for |
1225 |
|
|
example, select DMPC.3 |
1226 |
|
|
|
1227 |
gezelter |
2199 |
2005-02-07 16:11 tim |
1228 |
tim |
2102 |
|
1229 |
|
|
* src/applications/dump2Xyz/: Dump2XYZCmd.c, Dump2XYZCmd.h: update |
1230 |
|
|
help info for Dump2XYZ |
1231 |
|
|
|
1232 |
gezelter |
2199 |
2005-02-07 15:39 chrisfen |
1233 |
tim |
2102 |
|
1234 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
1235 |
|
|
selection librarys added |
1236 |
|
|
|
1237 |
gezelter |
2199 |
2005-02-07 15:31 tim |
1238 |
tim |
2102 |
|
1239 |
|
|
* src/selection/Makefile, make/Makefile.in: adding Makefile |
1240 |
|
|
|
1241 |
gezelter |
2199 |
2005-02-07 15:20 chrisfen |
1242 |
tim |
2102 |
|
1243 |
|
|
* src/utils/wildcards.hpp: issue commented out in wildcards |
1244 |
|
|
|
1245 |
gezelter |
2199 |
2005-02-07 15:06 tim |
1246 |
tim |
2102 |
|
1247 |
|
|
* src/selection/SelectionEvaluator.cpp: forget to reset the pc |
1248 |
|
|
which cause reevaluate return NULL |
1249 |
|
|
|
1250 |
gezelter |
2199 |
2005-02-07 14:14 tim |
1251 |
tim |
2102 |
|
1252 |
|
|
* src/brains/: SimCreator.cpp, SimSnapshotManager.cpp, |
1253 |
|
|
SimSnapshotManager.hpp: fix a bug in determing the global index for |
1254 |
|
|
rigidbodies |
1255 |
|
|
|
1256 |
gezelter |
2199 |
2005-02-07 14:13 tim |
1257 |
tim |
2102 |
|
1258 |
|
|
* src/utils/: BitSet.cpp, BitSet.hpp, StringUtils.hpp: minor change |
1259 |
|
|
in Bitset |
1260 |
|
|
|
1261 |
gezelter |
2199 |
2005-02-07 14:13 tim |
1262 |
tim |
2102 |
|
1263 |
|
|
* src/selection/: DistanceFinder.cpp, DistanceFinder.hpp, |
1264 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
1265 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.hpp, |
1266 |
|
|
TokenMap.cpp: selection library is working |
1267 |
|
|
|
1268 |
gezelter |
2199 |
2005-02-04 17:46 tim |
1269 |
tim |
2102 |
|
1270 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: remove SelectionVisitor |
1271 |
|
|
|
1272 |
gezelter |
2199 |
2005-02-04 17:45 tim |
1273 |
tim |
2102 |
|
1274 |
|
|
* src/visitors/: OtherVisitor.cpp, OtherVisitor.hpp: IgnoreVisitor |
1275 |
|
|
and XYZVisitor now use selection library |
1276 |
|
|
|
1277 |
gezelter |
2199 |
2005-02-04 17:44 tim |
1278 |
tim |
2102 |
|
1279 |
|
|
* src/brains/: MoleculeCreator.cpp, SimInfo.cpp, SimInfo.hpp: |
1280 |
|
|
adding SelectionManager into SimInfo |
1281 |
|
|
|
1282 |
gezelter |
2199 |
2005-02-04 17:43 tim |
1283 |
tim |
2102 |
|
1284 |
|
|
* src/applications/dump2Xyz/: Dump2XYZ.cpp, Dump2XYZ.ggo, |
1285 |
|
|
Dump2XYZCmd.c, Dump2XYZCmd.h: dump2Xyz now take advantage of |
1286 |
|
|
selection library |
1287 |
|
|
|
1288 |
gezelter |
2199 |
2005-02-04 17:42 tim |
1289 |
tim |
2102 |
|
1290 |
|
|
* src/utils/: BitSet.hpp, Makefile.in, wildcards.cpp: minor change |
1291 |
|
|
in BitSet |
1292 |
|
|
|
1293 |
gezelter |
2199 |
2005-02-04 17:41 tim |
1294 |
tim |
2102 |
|
1295 |
|
|
* src/primitives/: Molecule.hpp, RigidBody.hpp: adding missing |
1296 |
|
|
implementation |
1297 |
|
|
|
1298 |
gezelter |
2199 |
2005-02-04 17:39 tim |
1299 |
tim |
2102 |
|
1300 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
1301 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
1302 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
1303 |
|
|
SelectionManager.hpp, Token.hpp: half of the selection utility is |
1304 |
|
|
working need to debug within keyword and atomproperty keyword |
1305 |
|
|
|
1306 |
gezelter |
2199 |
2005-02-04 00:42 tim |
1307 |
tim |
2102 |
|
1308 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp: selection library |
1309 |
|
|
get built |
1310 |
|
|
|
1311 |
gezelter |
2199 |
2005-02-04 00:42 tim |
1312 |
tim |
2102 |
|
1313 |
|
|
* src/utils/: BitSet.cpp, BitSet.hpp: fix BitSet |
1314 |
|
|
|
1315 |
gezelter |
2199 |
2005-02-04 00:26 tim |
1316 |
tim |
2102 |
|
1317 |
|
|
* src/brains/: ForceFields.cpp, Migrator.hpp, SimCreator.cpp: |
1318 |
|
|
remove some useless files |
1319 |
|
|
|
1320 |
gezelter |
2199 |
2005-02-03 23:57 tim |
1321 |
tim |
2102 |
|
1322 |
|
|
* src/: primitives/RigidBody.hpp, selection/NameFinder.cpp, |
1323 |
|
|
selection/NameFinder.hpp, utils/wildcards.cpp, utils/wildcards.hpp: |
1324 |
|
|
adding wildcard class; NameFinder is finished |
1325 |
|
|
|
1326 |
gezelter |
2199 |
2005-02-03 18:14 tim |
1327 |
tim |
2102 |
|
1328 |
|
|
* src/selection/: NameFinder.cpp, NameFinder.hpp, |
1329 |
|
|
SelectionCompiler.cpp, SelectionCompiler.hpp, |
1330 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, |
1331 |
|
|
SelectionManager.hpp, Token.hpp, TokenMap.cpp: more work in |
1332 |
|
|
selection library |
1333 |
|
|
|
1334 |
gezelter |
2199 |
2005-02-03 09:04 tim |
1335 |
tim |
2102 |
|
1336 |
|
|
* src/selection/: SelectionEvaluator.cpp, SelectionEvaluator.hpp: |
1337 |
|
|
selection in progress |
1338 |
|
|
|
1339 |
gezelter |
2199 |
2005-02-02 18:13 tim |
1340 |
tim |
2102 |
|
1341 |
|
|
* src/selection/: SelectionCompiler.cpp, SelectionCompiler.hpp, |
1342 |
|
|
SelectionEvaluator.cpp, SelectionEvaluator.hpp, Token.cpp, |
1343 |
|
|
Token.hpp, TokenMap.cpp, TokenMap.hpp: selection library in |
1344 |
|
|
progress, except SelectionEvaluator, other files are compiled |
1345 |
|
|
|
1346 |
gezelter |
2199 |
2005-02-02 18:12 tim |
1347 |
tim |
2102 |
|
1348 |
|
|
* src/utils/: Makefile.in, any.hpp: adding boost::any |
1349 |
|
|
|
1350 |
gezelter |
2199 |
2005-02-02 07:51 tim |
1351 |
tim |
2102 |
|
1352 |
|
|
* src/selection/SelectionCompiler.cpp: add SelectionCompiler.cpp |
1353 |
|
|
|
1354 |
gezelter |
2199 |
2005-02-01 17:49 tim |
1355 |
tim |
2102 |
|
1356 |
|
|
* src/: utils/BitSet.cpp, utils/BitSet.hpp, utils/StringUtils.hpp, |
1357 |
|
|
selection/SelectionCompiler.hpp, selection/SelectionEvaluator.cpp, |
1358 |
|
|
selection/SelectionEvaluator.hpp, selection/SelectionManager.hpp, |
1359 |
|
|
selection/Token.hpp: Selection in progress |
1360 |
|
|
|
1361 |
gezelter |
2199 |
2005-02-01 01:55 tim |
1362 |
tim |
2102 |
|
1363 |
|
|
* src/: selection/SelectionCompiler.hpp, |
1364 |
|
|
selection/SelectionEvaluator.cpp, selection/SelectionEvaluator.hpp, |
1365 |
|
|
selection/SelectionManager.hpp, selection/Token.hpp, |
1366 |
|
|
utils/BitSet.cpp, utils/BitSet.hpp: adding selection library |
1367 |
|
|
|
1368 |
gezelter |
2199 |
2005-01-26 10:26 tim |
1369 |
tim |
2102 |
|
1370 |
|
|
* src/integrators/: Integrator.cpp, Integrator.hpp, |
1371 |
|
|
VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: forget |
1372 |
|
|
to add eorWriter |
1373 |
|
|
|
1374 |
gezelter |
2199 |
2005-01-26 10:15 tim |
1375 |
tim |
2102 |
|
1376 |
|
|
* src/: primitives/GhostTorsion.cpp, visitors/AtomVisitor.cpp: |
1377 |
|
|
(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the |
1378 |
|
|
wrong column of electroframe |
1379 |
|
|
|
1380 |
gezelter |
2199 |
2005-01-25 16:59 tim |
1381 |
tim |
2102 |
|
1382 |
|
|
* src/: brains/SimInfo.cpp, io/DumpReader.cpp: fix a bug in |
1383 |
|
|
SimInfo, use number of cutoff stamp as counter to loop over |
1384 |
|
|
rigidbody stamp |
1385 |
|
|
|
1386 |
gezelter |
2199 |
2005-01-25 12:45 tim |
1387 |
tim |
2102 |
|
1388 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
1389 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
1390 |
|
|
integrators/DLM.cpp, io/AtomTypesSectionParser.cpp, |
1391 |
|
|
io/BendTypesSectionParser.cpp, io/BondTypesSectionParser.cpp, |
1392 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, io/DumpReader.cpp, |
1393 |
|
|
io/EAMAtomTypesSectionParser.cpp, |
1394 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, io/Globals.cpp, |
1395 |
|
|
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
1396 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
1397 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
1398 |
|
|
math/SquareMatrix.hpp, primitives/DirectionalAtom.cpp, |
1399 |
|
|
primitives/DirectionalAtom.hpp, primitives/GhostTorsion.cpp, |
1400 |
|
|
primitives/GhostTorsion.hpp, primitives/Makefile, |
1401 |
|
|
primitives/RigidBody.cpp, types/MakeStamps.cpp: (1) complete |
1402 |
|
|
section parser's error message (2) add GhostTorsion (3) accumulate |
1403 |
|
|
inertial tensor from the directional atoms before calculate |
1404 |
|
|
rigidbody's inertial tensor |
1405 |
|
|
|
1406 |
gezelter |
2199 |
2005-01-17 17:17 tim |
1407 |
tim |
2102 |
|
1408 |
|
|
* forceFields/DUFF2.frc: forget to set dipole for lipid head group |
1409 |
|
|
|
1410 |
gezelter |
2199 |
2005-01-17 11:58 tim |
1411 |
tim |
2102 |
|
1412 |
|
|
* src/integrators/NVT.cpp: fix a bug in loading initial extended |
1413 |
|
|
system parameters |
1414 |
|
|
|
1415 |
gezelter |
2199 |
2005-01-17 11:05 tim |
1416 |
tim |
2102 |
|
1417 |
|
|
* src/integrators/NVT.cpp: forget to set maxIterNum_ in NVT |
1418 |
|
|
|
1419 |
gezelter |
2199 |
2005-01-14 17:02 tim |
1420 |
tim |
2102 |
|
1421 |
|
|
* src/UseTheForce/WATER.cpp: remove WATER.cpp |
1422 |
|
|
|
1423 |
gezelter |
2199 |
2005-01-14 16:37 tim |
1424 |
tim |
2102 |
|
1425 |
|
|
* forceFields/Makefile: sync Makefile |
1426 |
|
|
|
1427 |
gezelter |
2199 |
2005-01-14 16:13 gezelter |
1428 |
tim |
2102 |
|
1429 |
|
|
* make/Makefile.in, src/Makefile, src/UseTheForce/Makefile, |
1430 |
|
|
src/UseTheForce/DarkSide/Makefile, src/applications/Makefile, |
1431 |
|
|
src/applications/dump2Xyz/Makefile, |
1432 |
|
|
src/applications/oopse/Makefile, |
1433 |
|
|
src/applications/simpleBuilder/Makefile, src/brains/Makefile, |
1434 |
|
|
src/constraints/Makefile, src/integrators/Makefile, |
1435 |
|
|
src/io/Makefile, src/math/Makefile, src/minimizers/Makefile, |
1436 |
|
|
src/primitives/Makefile, src/profiling/Makefile, |
1437 |
|
|
src/restraints/Makefile, src/types/Makefile, src/utils/Makefile.in, |
1438 |
|
|
src/visitors/Makefile: moved Package variable into subdirectory |
1439 |
|
|
makefiles to speed up the building process |
1440 |
|
|
|
1441 |
gezelter |
2199 |
2005-01-14 15:48 gezelter |
1442 |
tim |
2102 |
|
1443 |
|
|
* src/applications/oopse/oopse.cpp: Fixed publication details in |
1444 |
|
|
banner |
1445 |
|
|
|
1446 |
gezelter |
2199 |
2005-01-14 15:48 gezelter |
1447 |
tim |
2102 |
|
1448 |
|
|
* src/UseTheForce/DarkSide/: simParallel_interface.F90, |
1449 |
|
|
simParallel_interface.h: added dummy subroutine to avoid empty |
1450 |
|
|
unit, synchronized this dummy routine between C and fortran |
1451 |
|
|
|
1452 |
gezelter |
2199 |
2005-01-14 15:31 gezelter |
1453 |
tim |
2102 |
|
1454 |
|
|
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.F90, |
1455 |
|
|
notifyCutoffs.F90, notifyCutoffs_interface.F90, DarkSide/LJ.F90, |
1456 |
|
|
DarkSide/Makefile, DarkSide/atype.F90, |
1457 |
|
|
DarkSide/atype_interface.F90, DarkSide/charge.F90, |
1458 |
|
|
DarkSide/charge_interface.F90, DarkSide/dipole.F90, |
1459 |
|
|
DarkSide/dipole_interface.F90, DarkSide/eam.F90, |
1460 |
|
|
DarkSide/eam_interface.F90, DarkSide/gb.F90, |
1461 |
|
|
DarkSide/gb_interface.F90, DarkSide/lj_interface.F90, |
1462 |
|
|
DarkSide/shapes.F90, DarkSide/shapes_interface.F90, |
1463 |
|
|
DarkSide/simParallel.F90, DarkSide/simParallel_interface.F90, |
1464 |
|
|
DarkSide/simulation.F90, DarkSide/simulation_interface.F90, |
1465 |
|
|
DarkSide/sticky.F90, DarkSide/sticky_interface.F90: separating |
1466 |
|
|
modules and C/Fortran interface subroutines |
1467 |
|
|
|
1468 |
gezelter |
2199 |
2005-01-14 15:15 gezelter |
1469 |
tim |
2102 |
|
1470 |
|
|
* configure, ac-tools/aclocal.m4: more fixes for gnugetopt |
1471 |
|
|
|
1472 |
gezelter |
2199 |
2005-01-14 15:09 gezelter |
1473 |
tim |
2102 |
|
1474 |
|
|
* configure, ac-tools/configure.in, src/config.h.in, |
1475 |
|
|
src/utils/Makefile, src/utils/Makefile.in: fixing for gnugetopt |
1476 |
|
|
|
1477 |
gezelter |
2199 |
2005-01-14 11:49 tim |
1478 |
tim |
2102 |
|
1479 |
|
|
* src/: io/EAMAtomTypesSectionParser.cpp, |
1480 |
|
|
utils/StringTokenizer.cpp, utils/StringTokenizer.hpp, |
1481 |
|
|
utils/StringUtils.hpp: using c library to do conversion instead of |
1482 |
|
|
using iostream due to a bug in libstdc++(GCC 3.2) |
1483 |
|
|
|
1484 |
gezelter |
2199 |
2005-01-13 21:40 tim |
1485 |
tim |
2102 |
|
1486 |
|
|
* src/brains/SimSetup.cpp: no message |
1487 |
|
|
|
1488 |
gezelter |
2199 |
2005-01-13 20:56 tim |
1489 |
tim |
2102 |
|
1490 |
|
|
* src/primitives/Molecule.hpp: fix a bug in global index |
1491 |
|
|
|
1492 |
gezelter |
2199 |
2005-01-13 20:04 tim |
1493 |
tim |
2102 |
|
1494 |
|
|
* src/minimizers/: Minimizer.cpp, Minimizer.hpp: remove include |
1495 |
|
|
Integrator.hpp in Minimizer |
1496 |
|
|
|
1497 |
gezelter |
2199 |
2005-01-13 17:14 gezelter |
1498 |
tim |
2102 |
|
1499 |
|
|
* src/utils/Makefile: compile getopt and getopt1 if we need to |
1500 |
|
|
|
1501 |
gezelter |
2199 |
2005-01-13 16:56 gezelter |
1502 |
tim |
2102 |
|
1503 |
|
|
* make/Makefile.in: template flags |
1504 |
|
|
|
1505 |
gezelter |
2199 |
2005-01-13 16:48 gezelter |
1506 |
tim |
2102 |
|
1507 |
|
|
* src/applications/oopse/Makefile: formatting |
1508 |
|
|
|
1509 |
gezelter |
2199 |
2005-01-13 16:48 gezelter |
1510 |
tim |
2102 |
|
1511 |
|
|
* make/Makefile.in: fixed a MakeDir / MkDir problem added BinDir |
1512 |
|
|
target |
1513 |
|
|
|
1514 |
gezelter |
2199 |
2005-01-13 14:40 tim |
1515 |
tim |
2102 |
|
1516 |
|
|
* src/: UseTheForce/fSwitchingFunction.h, |
1517 |
|
|
UseTheForce/mpiComponentPlan.h, brains/fSimulation.h, io/Makefile, |
1518 |
|
|
math/Makefile, math/RectMatrix.hpp, math/Vector.hpp, |
1519 |
|
|
primitives/RigidBody.cpp, types/AtomTypeProperties.h, |
1520 |
|
|
types/CharmmTorsionType.cpp, utils/simError.h: port to SGI platform |
1521 |
|
|
|
1522 |
gezelter |
2199 |
2005-01-13 13:26 tim |
1523 |
tim |
2102 |
|
1524 |
|
|
* make/Makefile.in: change the order of linking (object file comes |
1525 |
|
|
first and then follow by user built library) |
1526 |
|
|
|
1527 |
gezelter |
2199 |
2005-01-12 18:24 tim |
1528 |
tim |
2102 |
|
1529 |
|
|
* src/io/DumpWriter.cpp: remove useless debug info |
1530 |
|
|
|
1531 |
gezelter |
2199 |
2005-01-12 18:21 tim |
1532 |
tim |
2102 |
|
1533 |
|
|
* src/applications/dump2Xyz/Dump2XYZ.cpp: minor fix |
1534 |
|
|
|
1535 |
gezelter |
2199 |
2005-01-12 18:17 tim |
1536 |
tim |
2102 |
|
1537 |
|
|
* make/: Makefile.in, Makefile.in: missing tab |
1538 |
|
|
|
1539 |
gezelter |
2199 |
2005-01-12 18:15 tim |
1540 |
tim |
2102 |
|
1541 |
|
|
* src/visitors/: AtomVisitor.cpp, AtomVisitor.hpp: LinearVisitor |
1542 |
|
|
get fixed |
1543 |
|
|
|
1544 |
gezelter |
2199 |
2005-01-12 17:40 gezelter |
1545 |
tim |
2102 |
|
1546 |
|
|
* make/Makefile.in, src/UseTheForce/DUFF.cpp, |
1547 |
|
|
src/UseTheForce/DUFF.hpp, src/UseTheForce/EAM.cpp, |
1548 |
|
|
src/UseTheForce/EAM.hpp, src/UseTheForce/EAM_FF.cpp, |
1549 |
|
|
src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp, |
1550 |
|
|
src/UseTheForce/ForceFieldCreator.hpp, |
1551 |
|
|
src/UseTheForce/ForceFieldFactory.cpp, |
1552 |
|
|
src/UseTheForce/ForceFieldFactory.hpp, src/UseTheForce/LJFF.cpp, |
1553 |
|
|
src/UseTheForce/Makefile, src/UseTheForce/Shapes_FF.cpp, |
1554 |
|
|
src/UseTheForce/doForces.F90, src/UseTheForce/doForces_interface.h, |
1555 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
1556 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
1557 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
1558 |
|
|
src/UseTheForce/notifyCutoffs.F90, |
1559 |
|
|
src/UseTheForce/notifyCutoffs_interface.h, |
1560 |
|
|
src/UseTheForce/DarkSide/LJ.F90, |
1561 |
|
|
src/UseTheForce/DarkSide/atype.F90, |
1562 |
|
|
src/UseTheForce/DarkSide/atype_interface.h, |
1563 |
|
|
src/UseTheForce/DarkSide/charge.F90, |
1564 |
|
|
src/UseTheForce/DarkSide/charge_interface.h, |
1565 |
|
|
src/UseTheForce/DarkSide/dipole.F90, |
1566 |
|
|
src/UseTheForce/DarkSide/dipole_interface.h, |
1567 |
|
|
src/UseTheForce/DarkSide/eam.F90, |
1568 |
|
|
src/UseTheForce/DarkSide/eam_interface.h, |
1569 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
1570 |
|
|
src/UseTheForce/DarkSide/gb.F90, |
1571 |
|
|
src/UseTheForce/DarkSide/gb_interface.h, |
1572 |
|
|
src/UseTheForce/DarkSide/lj_interface.h, |
1573 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
1574 |
|
|
src/UseTheForce/DarkSide/reactionField.F90, |
1575 |
|
|
src/UseTheForce/DarkSide/shapes.F90, |
1576 |
|
|
src/UseTheForce/DarkSide/shapes_interface.h, |
1577 |
|
|
src/UseTheForce/DarkSide/simParallel.F90, |
1578 |
|
|
src/UseTheForce/DarkSide/simParallel_interface.h, |
1579 |
|
|
src/UseTheForce/DarkSide/simulation.F90, |
1580 |
|
|
src/UseTheForce/DarkSide/simulation_interface.h, |
1581 |
|
|
src/UseTheForce/DarkSide/sticky.F90, |
1582 |
|
|
src/UseTheForce/DarkSide/sticky_interface.h, |
1583 |
|
|
src/UseTheForce/DarkSide/switcheroo.F90, |
1584 |
|
|
src/applications/Makedepend, src/applications/quickLate.c, |
1585 |
|
|
src/applications/dump2Xyz/Dump2XYZ.cpp, |
1586 |
|
|
src/applications/oopse/oopse.cpp, |
1587 |
|
|
src/applications/simpleBuilder/BaseLattice.cpp, |
1588 |
|
|
src/applications/simpleBuilder/BaseLattice.hpp, |
1589 |
|
|
src/applications/simpleBuilder/Lattice.cpp, |
1590 |
|
|
src/applications/simpleBuilder/Lattice.hpp, |
1591 |
|
|
src/applications/simpleBuilder/LatticeCreator.cpp, |
1592 |
|
|
src/applications/simpleBuilder/LatticeCreator.hpp, |
1593 |
|
|
src/applications/simpleBuilder/LatticeFactory.cpp, |
1594 |
|
|
src/applications/simpleBuilder/LatticeFactory.hpp, |
1595 |
|
|
src/applications/simpleBuilder/MoLocator.cpp, |
1596 |
|
|
src/applications/simpleBuilder/MoLocator.hpp, |
1597 |
|
|
src/applications/simpleBuilder/simpleBuilder.cpp, |
1598 |
|
|
src/brains/DataStorage.cpp, src/brains/DataStorage.hpp, |
1599 |
|
|
src/brains/Exclude.cpp, src/brains/Exclude.hpp, |
1600 |
|
|
src/brains/ForceManager.cpp, src/brains/ForceManager.hpp, |
1601 |
|
|
src/brains/Makefile, src/brains/Migrator.hpp, |
1602 |
|
|
src/brains/MoleculeCreator.cpp, src/brains/MoleculeCreator.hpp, |
1603 |
|
|
src/brains/Register.cpp, src/brains/Register.hpp, |
1604 |
|
|
src/brains/SimCreator.cpp, src/brains/SimCreator.hpp, |
1605 |
|
|
src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
1606 |
|
|
src/brains/SimModel.hpp, src/brains/SimSetup.hpp, |
1607 |
|
|
src/brains/SimSnapshotManager.cpp, |
1608 |
|
|
src/brains/SimSnapshotManager.hpp, src/brains/SimState.cpp, |
1609 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
1610 |
|
|
src/brains/SkipList.hpp, src/brains/Snapshot.cpp, |
1611 |
|
|
src/brains/Snapshot.hpp, src/brains/SnapshotManager.hpp, |
1612 |
|
|
src/brains/Stats.cpp, src/brains/Stats.hpp, src/brains/Thermo.cpp, |
1613 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
1614 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
1615 |
|
|
src/constraints/AbstractClasses.hpp, |
1616 |
|
|
src/constraints/ConstraintElem.hpp, |
1617 |
|
|
src/constraints/ConstraintPair.hpp, src/constraints/Makefile, |
1618 |
|
|
src/constraints/Rattle.cpp, src/constraints/Rattle.hpp, |
1619 |
|
|
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
1620 |
|
|
src/constraints/ZconsStruct.hpp, |
1621 |
|
|
src/constraints/ZconstraintForceManager.cpp, |
1622 |
|
|
src/constraints/ZconstraintForceManager.hpp, |
1623 |
|
|
src/integrators/AbstractClasses.hpp, |
1624 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/DLM.cpp, |
1625 |
|
|
src/integrators/DLM.hpp, src/integrators/Integrator.cpp, |
1626 |
|
|
src/integrators/Integrator.hpp, |
1627 |
|
|
src/integrators/IntegratorCreator.hpp, |
1628 |
|
|
src/integrators/IntegratorFactory.cpp, |
1629 |
|
|
src/integrators/IntegratorFactory.hpp, src/integrators/Makefile, |
1630 |
|
|
src/integrators/NPT.cpp, src/integrators/NPT.hpp, |
1631 |
|
|
src/integrators/NPTf.cpp, src/integrators/NPTf.hpp, |
1632 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTi.hpp, |
1633 |
|
|
src/integrators/NPTxyz.cpp, src/integrators/NPTxyz.hpp, |
1634 |
|
|
src/integrators/NVE.cpp, src/integrators/NVE.hpp, |
1635 |
|
|
src/integrators/NVT.cpp, src/integrators/NVT.hpp, |
1636 |
|
|
src/integrators/RotationAlgorithm.hpp, |
1637 |
|
|
src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp, |
1638 |
|
|
src/integrators/VelocityVerletIntegrator.cpp, |
1639 |
|
|
src/integrators/VelocityVerletIntegrator.hpp, |
1640 |
|
|
src/io/AtomTypesSectionParser.cpp, |
1641 |
|
|
src/io/AtomTypesSectionParser.hpp, src/io/BASS_interface.cpp, |
1642 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
1643 |
|
|
src/io/BendTypesSectionParser.cpp, |
1644 |
|
|
src/io/BendTypesSectionParser.hpp, |
1645 |
|
|
src/io/BondTypesSectionParser.cpp, |
1646 |
|
|
src/io/BondTypesSectionParser.hpp, |
1647 |
|
|
src/io/DirectionalAtomTypesSectionParser.cpp, |
1648 |
|
|
src/io/DirectionalAtomTypesSectionParser.hpp, |
1649 |
|
|
src/io/DumpReader.cpp, src/io/DumpReader.hpp, |
1650 |
|
|
src/io/DumpWriter.cpp, src/io/DumpWriter.hpp, |
1651 |
|
|
src/io/EAMAtomTypesSectionParser.cpp, |
1652 |
|
|
src/io/EAMAtomTypesSectionParser.hpp, |
1653 |
|
|
src/io/ElectrostaticAtomTypesSectionParser.cpp, |
1654 |
|
|
src/io/ElectrostaticAtomTypesSectionParser.hpp, src/io/Globals.cpp, |
1655 |
|
|
src/io/Globals.hpp, src/io/InitializeFromFile.cpp, |
1656 |
|
|
src/io/LennardJonesAtomTypesSectionParser.cpp, |
1657 |
|
|
src/io/LennardJonesAtomTypesSectionParser.hpp, |
1658 |
|
|
src/io/LinkedAssign.cpp, src/io/LinkedAssign.hpp, |
1659 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
1660 |
|
|
src/io/Makefile, src/io/SectionParser.cpp, |
1661 |
|
|
src/io/SectionParser.hpp, src/io/SectionParserManager.cpp, |
1662 |
|
|
src/io/SectionParserManager.hpp, src/io/StatWriter.cpp, |
1663 |
|
|
src/io/StatWriter.hpp, src/io/StickyAtomTypesSectionParser.cpp, |
1664 |
|
|
src/io/StickyAtomTypesSectionParser.hpp, |
1665 |
|
|
src/io/TorsionTypesSectionParser.cpp, |
1666 |
|
|
src/io/TorsionTypesSectionParser.hpp, src/io/ZConsReader.cpp, |
1667 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
1668 |
|
|
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
1669 |
|
|
src/io/interface.c, src/io/make_nodes.c, src/io/make_nodes.h, |
1670 |
|
|
src/io/mpiBASS.c, src/io/mpiBASS.h, src/io/node_list.h, |
1671 |
|
|
src/io/parse_interface.h, src/io/parse_me.h, src/io/parse_tree.c, |
1672 |
|
|
src/io/parse_tree.h, src/math/ChebyshevPolynomials.cpp, |
1673 |
|
|
src/math/ChebyshevPolynomials.hpp, src/math/MatVec3.c, |
1674 |
|
|
src/math/MatVec3.h, src/math/Polynomial.hpp, |
1675 |
|
|
src/math/Quaternion.hpp, src/math/RealSphericalHarmonic.cpp, |
1676 |
|
|
src/math/RealSphericalHarmonic.hpp, src/math/RectMatrix.hpp, |
1677 |
|
|
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
1678 |
|
|
src/math/Vector.hpp, src/math/Vector3.hpp, |
1679 |
|
|
src/math/randomSPRNG.cpp, src/math/randomSPRNG.hpp, |
1680 |
|
|
src/minimizers/CGFamilyMinimizer.cpp, |
1681 |
|
|
src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Makefile, |
1682 |
|
|
src/minimizers/Minimizer.cpp, src/minimizers/Minimizer.hpp, |
1683 |
|
|
src/minimizers/MinimizerCreator.hpp, |
1684 |
|
|
src/minimizers/MinimizerFactory.cpp, |
1685 |
|
|
src/minimizers/MinimizerFactory.hpp, |
1686 |
|
|
src/minimizers/MinimizerParameterSet.cpp, |
1687 |
|
|
src/minimizers/MinimizerParameterSet.hpp, |
1688 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
1689 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
1690 |
|
|
src/minimizers/PRCG.hpp, src/minimizers/SDMinimizer.cpp, |
1691 |
|
|
src/minimizers/SDMinimizer.hpp, src/primitives/AbstractClasses.hpp, |
1692 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
1693 |
|
|
src/primitives/Bend.cpp, src/primitives/Bend.hpp, |
1694 |
|
|
src/primitives/BendExtensions.cpp, src/primitives/Bond.cpp, |
1695 |
|
|
src/primitives/Bond.hpp, src/primitives/BondExtensions.cpp, |
1696 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
1697 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
1698 |
|
|
src/primitives/GhostBend.hpp, src/primitives/Makefile, |
1699 |
|
|
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
1700 |
|
|
src/primitives/RigidBody.cpp, src/primitives/RigidBody.hpp, |
1701 |
|
|
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
1702 |
|
|
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
1703 |
|
|
src/primitives/Torsion.hpp, src/primitives/TorsionExtensions.cpp, |
1704 |
|
|
src/primitives/UreyBradleyBend.cpp, |
1705 |
|
|
src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp, |
1706 |
|
|
src/profiling/mdProfile.hpp, src/types/AtomStamp.cpp, |
1707 |
|
|
src/types/AtomStamp.hpp, src/types/AtomType.cpp, |
1708 |
|
|
src/types/AtomType.hpp, src/types/AtomTypeProperties.h, |
1709 |
|
|
src/types/BendStamp.cpp, src/types/BendStamp.hpp, |
1710 |
|
|
src/types/BendType.hpp, src/types/BondStamp.cpp, |
1711 |
|
|
src/types/BondStamp.hpp, src/types/BondType.hpp, |
1712 |
|
|
src/types/CharmmTorsionType.cpp, src/types/CharmmTorsionType.hpp, |
1713 |
|
|
src/types/Component.cpp, src/types/Component.hpp, |
1714 |
|
|
src/types/CubicBendType.hpp, src/types/CubicBondType.hpp, |
1715 |
|
|
src/types/CubicTorsionType.hpp, src/types/CutoffGroupStamp.cpp, |
1716 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/DirectionalAtomType.cpp, |
1717 |
|
|
src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp, |
1718 |
|
|
src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp, |
1719 |
|
|
src/types/MakeStamps.cpp, src/types/MakeStamps.hpp, |
1720 |
|
|
src/types/Makefile, src/types/MoleculeStamp.cpp, |
1721 |
|
|
src/types/MoleculeStamp.hpp, src/types/MorseBondType.hpp, |
1722 |
|
|
src/types/OplsTorsionType.hpp, src/types/PolynomialBendType.hpp, |
1723 |
|
|
src/types/PolynomialBondType.hpp, |
1724 |
|
|
src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp, |
1725 |
|
|
src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp, |
1726 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
1727 |
|
|
src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp, |
1728 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
1729 |
|
|
src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp, |
1730 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
1731 |
|
|
src/utils/GenericData.hpp, src/utils/GenericFactory.hpp, |
1732 |
|
|
src/utils/LocalIndexManager.hpp, src/utils/Makefile, |
1733 |
|
|
src/utils/MemoryUtils.hpp, src/utils/NumericConstant.hpp, |
1734 |
|
|
src/utils/OOPSEConstant.hpp, src/utils/PropertyMap.cpp, |
1735 |
|
|
src/utils/PropertyMap.hpp, src/utils/StreamTokenizer.cpp, |
1736 |
|
|
src/utils/StreamTokenizer.hpp, src/utils/StringTokenizer.cpp, |
1737 |
|
|
src/utils/StringTokenizer.hpp, src/utils/StringUtils.cpp, |
1738 |
|
|
src/utils/StringUtils.hpp, src/utils/Trim.cpp, src/utils/Trim.hpp, |
1739 |
|
|
src/utils/Tuple.hpp, src/utils/TupleMatcher.hpp, |
1740 |
|
|
src/utils/TypeContainer.hpp, src/utils/TypeInfo.hpp, |
1741 |
|
|
src/utils/Utility.cpp, src/utils/Utility.hpp, |
1742 |
|
|
src/utils/definitions.F90, src/utils/fError.c, |
1743 |
|
|
src/utils/next_combination.hpp, src/utils/oopseMPI.F90, |
1744 |
|
|
src/utils/simError.c, src/utils/simError.h, src/utils/status.F90, |
1745 |
|
|
src/utils/vector_class.F90, src/visitors/AtomData.hpp, |
1746 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
1747 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
1748 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
1749 |
|
|
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
1750 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
1751 |
|
|
src/visitors/ZconsVisitor.hpp: merging new_design branch into |
1752 |
|
|
OOPSE-2.0 |
1753 |
|
|
|
1754 |
gezelter |
2199 |
2005-01-12 13:13 tim |
1755 |
tim |
2102 |
|
1756 |
|
|
* src/: io/SectionParserManager.cpp, primitives/RigidBody.cpp, |
1757 |
|
|
utils/TypeContainer.hpp: forget to include <algorithm> |
1758 |
|
|
|
1759 |
gezelter |
2199 |
2005-01-12 12:25 tim |
1760 |
tim |
2102 |
|
1761 |
|
|
* forceFields/: DUFF.frc, DipoleTest.frc, LJFF.frc, newEAM.VC.frc, |
1762 |
|
|
newEAM.frc, newEAM.u3.frc, newEAM.u6.frc: remove some useless force |
1763 |
|
|
fields |
1764 |
|
|
|
1765 |
gezelter |
2199 |
2005-01-12 12:14 tim |
1766 |
tim |
2102 |
|
1767 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
1768 |
|
|
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
1769 |
|
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
1770 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
1771 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
1772 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Shapes_FF.cpp, |
1773 |
|
|
UseTheForce/doForces.F90, UseTheForce/doForces_interface.h, |
1774 |
|
|
UseTheForce/fSwitchingFunction.h, UseTheForce/mpiComponentPlan.h, |
1775 |
|
|
UseTheForce/notifyCutoffs.F90, |
1776 |
|
|
UseTheForce/notifyCutoffs_interface.h, UseTheForce/DarkSide/LJ.F90, |
1777 |
|
|
UseTheForce/DarkSide/atype.F90, |
1778 |
|
|
UseTheForce/DarkSide/atype_interface.h, |
1779 |
|
|
UseTheForce/DarkSide/charge.F90, |
1780 |
|
|
UseTheForce/DarkSide/charge_interface.h, |
1781 |
|
|
UseTheForce/DarkSide/dipole.F90, |
1782 |
|
|
UseTheForce/DarkSide/dipole_interface.h, |
1783 |
|
|
UseTheForce/DarkSide/eam.F90, UseTheForce/DarkSide/eam_interface.h, |
1784 |
|
|
UseTheForce/DarkSide/force_globals.F90, |
1785 |
|
|
UseTheForce/DarkSide/gb.F90, UseTheForce/DarkSide/gb_interface.h, |
1786 |
|
|
UseTheForce/DarkSide/lj_interface.h, |
1787 |
|
|
UseTheForce/DarkSide/neighborLists.F90, |
1788 |
|
|
UseTheForce/DarkSide/reactionField.F90, |
1789 |
|
|
UseTheForce/DarkSide/shapes.F90, |
1790 |
|
|
UseTheForce/DarkSide/shapes_interface.h, |
1791 |
|
|
UseTheForce/DarkSide/simParallel.F90, |
1792 |
|
|
UseTheForce/DarkSide/simParallel_interface.h, |
1793 |
|
|
UseTheForce/DarkSide/simulation.F90, |
1794 |
|
|
UseTheForce/DarkSide/simulation_interface.h, |
1795 |
|
|
UseTheForce/DarkSide/sticky.F90, |
1796 |
|
|
UseTheForce/DarkSide/sticky_interface.h, |
1797 |
|
|
UseTheForce/DarkSide/switcheroo.F90, |
1798 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
1799 |
|
|
applications/simpleBuilder/BaseLattice.cpp, |
1800 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
1801 |
|
|
applications/simpleBuilder/Lattice.cpp, |
1802 |
|
|
applications/simpleBuilder/Lattice.hpp, |
1803 |
|
|
applications/simpleBuilder/LatticeCreator.cpp, |
1804 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
1805 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
1806 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
1807 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
1808 |
|
|
applications/simpleBuilder/MoLocator.hpp, |
1809 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
1810 |
|
|
brains/DataStorage.cpp, brains/DataStorage.hpp, brains/Exclude.cpp, |
1811 |
|
|
brains/Exclude.hpp, brains/ForceManager.cpp, |
1812 |
|
|
brains/ForceManager.hpp, brains/Makefile, brains/Migrator.hpp, |
1813 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
1814 |
|
|
brains/Register.cpp, brains/Register.hpp, brains/SimCreator.cpp, |
1815 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
1816 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
1817 |
|
|
brains/SkipList.cpp, brains/SkipList.hpp, brains/SnapShot.cpp, |
1818 |
|
|
brains/Snapshot.cpp, brains/Snapshot.hpp, |
1819 |
|
|
brains/SnapshotManager.hpp, brains/Stats.cpp, brains/Stats.hpp, |
1820 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, brains/fSimulation.h, |
1821 |
|
|
constraints/ConstraintElem.hpp, constraints/ConstraintPair.hpp, |
1822 |
|
|
constraints/Rattle.cpp, constraints/Rattle.hpp, |
1823 |
|
|
constraints/ZconsStruct.hpp, |
1824 |
|
|
constraints/ZconstraintForceManager.cpp, |
1825 |
|
|
constraints/ZconstraintForceManager.hpp, integrators/DLM.cpp, |
1826 |
|
|
integrators/DLM.hpp, integrators/Integrator.cpp, |
1827 |
|
|
integrators/Integrator.hpp, integrators/IntegratorCreator.hpp, |
1828 |
|
|
integrators/IntegratorFactory.cpp, |
1829 |
|
|
integrators/IntegratorFactory.hpp, integrators/NPT.cpp, |
1830 |
|
|
integrators/NPT.hpp, integrators/NPTf.cpp, integrators/NPTf.hpp, |
1831 |
|
|
integrators/NPTi.cpp, integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
1832 |
|
|
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
1833 |
|
|
integrators/NVT.cpp, integrators/NVT.hpp, |
1834 |
|
|
integrators/RotationAlgorithm.hpp, integrators/Velocitizer.cpp, |
1835 |
|
|
integrators/Velocitizer.hpp, |
1836 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
1837 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
1838 |
|
|
io/AtomTypesSectionParser.cpp, io/AtomTypesSectionParser.hpp, |
1839 |
|
|
io/BASS_interface.cpp, io/BASS_interface.h, io/BASS_parse.c, |
1840 |
|
|
io/BASS_parse.h, io/BendTypesSectionParser.cpp, |
1841 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
1842 |
|
|
io/BondTypesSectionParser.hpp, |
1843 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
1844 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
1845 |
|
|
io/DumpReader.hpp, io/DumpWriter.cpp, io/DumpWriter.hpp, |
1846 |
|
|
io/EAMAtomTypesSectionParser.cpp, io/EAMAtomTypesSectionParser.hpp, |
1847 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
1848 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/Globals.cpp, |
1849 |
|
|
io/Globals.hpp, io/LennardJonesAtomTypesSectionParser.cpp, |
1850 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/LinkedAssign.cpp, |
1851 |
|
|
io/LinkedAssign.hpp, io/LinkedCommand.cpp, io/LinkedCommand.hpp, |
1852 |
|
|
io/SectionParser.cpp, io/SectionParser.hpp, |
1853 |
|
|
io/SectionParserManager.cpp, io/SectionParserManager.hpp, |
1854 |
|
|
io/StatWriter.cpp, io/StatWriter.hpp, |
1855 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
1856 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
1857 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
1858 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
1859 |
|
|
io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, io/interface.c, |
1860 |
|
|
io/make_nodes.c, io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, |
1861 |
|
|
io/node_list.h, io/parse_interface.h, io/parse_me.h, |
1862 |
|
|
io/parse_tree.c, io/parse_tree.h, math/ChebyshevPolynomials.cpp, |
1863 |
|
|
math/ChebyshevPolynomials.hpp, math/MatVec3.c, math/MatVec3.h, |
1864 |
|
|
math/Polynomial.hpp, math/Quaternion.hpp, |
1865 |
|
|
math/RealSphericalHarmonic.cpp, math/RealSphericalHarmonic.hpp, |
1866 |
|
|
math/RectMatrix.hpp, math/SquareMatrix.hpp, math/SquareMatrix3.hpp, |
1867 |
|
|
math/Vector.hpp, math/Vector3.hpp, math/randomSPRNG.cpp, |
1868 |
|
|
math/randomSPRNG.hpp, minimizers/CGFamilyMinimizer.cpp, |
1869 |
|
|
minimizers/CGFamilyMinimizer.hpp, minimizers/Minimizer.cpp, |
1870 |
|
|
minimizers/Minimizer.hpp, minimizers/MinimizerCreator.hpp, |
1871 |
|
|
minimizers/MinimizerFactory.cpp, minimizers/MinimizerFactory.hpp, |
1872 |
|
|
minimizers/MinimizerParameterSet.cpp, |
1873 |
|
|
minimizers/MinimizerParameterSet.hpp, minimizers/PRCG.cpp, |
1874 |
|
|
minimizers/PRCG.hpp, minimizers/SDMinimizer.cpp, |
1875 |
|
|
minimizers/SDMinimizer.hpp, primitives/Atom.cpp, |
1876 |
|
|
primitives/Atom.hpp, primitives/Bend.cpp, primitives/Bend.hpp, |
1877 |
|
|
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
1878 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
1879 |
|
|
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
1880 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp, |
1881 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
1882 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
1883 |
|
|
primitives/Torsion.cpp, primitives/Torsion.hpp, |
1884 |
|
|
primitives/UreyBradleyBend.cpp, primitives/UreyBradleyBend.hpp, |
1885 |
|
|
profiling/mdProfile.cpp, profiling/mdProfile.hpp, |
1886 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp, |
1887 |
|
|
types/AtomStamp.cpp, types/AtomStamp.hpp, types/AtomType.cpp, |
1888 |
|
|
types/AtomType.hpp, types/AtomTypeProperties.h, |
1889 |
|
|
types/BendStamp.cpp, types/BendStamp.hpp, types/BendType.hpp, |
1890 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/BondType.hpp, |
1891 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
1892 |
|
|
types/Component.cpp, types/Component.hpp, types/CubicBendType.hpp, |
1893 |
|
|
types/CubicBondType.hpp, types/CubicTorsionType.hpp, |
1894 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
1895 |
|
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp, |
1896 |
|
|
types/FixedBondType.hpp, types/HarmonicBendType.hpp, |
1897 |
|
|
types/HarmonicBondType.hpp, types/MakeStamps.cpp, |
1898 |
|
|
types/MakeStamps.hpp, types/MoleculeStamp.cpp, |
1899 |
|
|
types/MoleculeStamp.hpp, types/MorseBondType.hpp, |
1900 |
|
|
types/OplsTorsionType.hpp, types/PolynomialBendType.hpp, |
1901 |
|
|
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
1902 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp, |
1903 |
|
|
types/QuarticTorsionType.hpp, types/RigidBodyStamp.cpp, |
1904 |
|
|
types/RigidBodyStamp.hpp, types/ShapeAtomType.cpp, |
1905 |
|
|
types/ShapeAtomType.hpp, types/TorsionStamp.cpp, |
1906 |
|
|
types/TorsionStamp.hpp, types/TorsionType.hpp, |
1907 |
|
|
types/UreyBradleyBendType.hpp, types/ZconStamp.cpp, |
1908 |
|
|
types/ZconStamp.hpp, utils/GenericData.hpp, |
1909 |
|
|
utils/GenericFactory.hpp, utils/LocalIndexManager.hpp, |
1910 |
|
|
utils/MemoryUtils.hpp, utils/NumericConstant.hpp, |
1911 |
|
|
utils/OOPSEConstant.hpp, utils/PropertyMap.cpp, |
1912 |
|
|
utils/PropertyMap.hpp, utils/StringTokenizer.cpp, |
1913 |
|
|
utils/StringTokenizer.hpp, utils/StringUtils.cpp, |
1914 |
|
|
utils/StringUtils.hpp, utils/Trim.cpp, utils/Trim.hpp, |
1915 |
|
|
utils/Tuple.hpp, utils/TupleMatcher.hpp, utils/TypeContainer.hpp, |
1916 |
|
|
utils/Utility.cpp, utils/Utility.hpp, utils/definitions.F90, |
1917 |
|
|
utils/fError.c, utils/next_combination.hpp, utils/oopseMPI.F90, |
1918 |
|
|
utils/simError.c, utils/simError.h, utils/status.F90, |
1919 |
|
|
utils/vector_class.F90, visitors/AtomData.hpp, |
1920 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp, |
1921 |
|
|
visitors/BaseVisitor.hpp, visitors/CompositeVisitor.cpp, |
1922 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
1923 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
1924 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
1925 |
|
|
visitors/ZconsVisitor.hpp: change license |
1926 |
|
|
|
1927 |
gezelter |
2199 |
2005-01-12 12:14 tim |
1928 |
tim |
2102 |
|
1929 |
|
|
* src/brains/Snapshot.cpp: file Snapshot.cpp was initially added on |
1930 |
|
|
branch new_design. |
1931 |
|
|
|
1932 |
gezelter |
2199 |
2005-01-11 16:03 tim |
1933 |
tim |
2102 |
|
1934 |
|
|
* src/: constraints/ZconstraintForceManager.cpp, |
1935 |
|
|
constraints/ZconstraintForceManager.hpp, |
1936 |
|
|
minimizers/MinimizerParameterSet.cpp, |
1937 |
|
|
minimizers/MinimizerParameterSet.hpp: change const static double |
1938 |
|
|
data member to const double |
1939 |
|
|
|
1940 |
gezelter |
2199 |
2005-01-11 15:50 tim |
1941 |
tim |
2102 |
|
1942 |
|
|
* src/io/basic_ifstrstream.hpp: forget namespace qualifier std:: |
1943 |
|
|
|
1944 |
gezelter |
2199 |
2005-01-11 15:39 tim |
1945 |
tim |
2102 |
|
1946 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, types/AtomTypeProperties.h: |
1947 |
|
|
change data type from logical to integer in AtomTypeProperties.h |
1948 |
|
|
|
1949 |
gezelter |
2199 |
2005-01-11 11:36 tim |
1950 |
tim |
2102 |
|
1951 |
|
|
* forceFields/: EAM.VC.frc, EAM.frc, EAM.u3.frc, EAM.u6.frc: adding |
1952 |
|
|
new format of EAM force field |
1953 |
|
|
|
1954 |
gezelter |
2199 |
2005-01-11 11:24 tim |
1955 |
tim |
2102 |
|
1956 |
|
|
* src/UseTheForce/DUFF.cpp: change default name of DUFF force field |
1957 |
|
|
to DUFF2.frc |
1958 |
|
|
|
1959 |
gezelter |
2199 |
2005-01-11 11:23 tim |
1960 |
tim |
2102 |
|
1961 |
|
|
* forceFields/: DUFF2.frc, newDUFF.frc: rename newDUFF.frc to |
1962 |
|
|
DUFF2.frc |
1963 |
|
|
|
1964 |
gezelter |
2199 |
2005-01-11 11:09 tim |
1965 |
tim |
2102 |
|
1966 |
|
|
* make/Makefile.in: adding constraints and minimizers into |
1967 |
|
|
Makefile.in |
1968 |
|
|
|
1969 |
gezelter |
2199 |
2005-01-11 11:03 tim |
1970 |
tim |
2102 |
|
1971 |
|
|
* src/io/: ChargeAtomTypesSectionParser.cpp, |
1972 |
|
|
ChargeAtomTypesSectionParser.hpp, DipoleAtomTypesSectionParser.cpp, |
1973 |
|
|
DipoleAtomTypesSectionParser.hpp, Makefile: remove some useless |
1974 |
|
|
files |
1975 |
|
|
|
1976 |
gezelter |
2199 |
2005-01-11 10:59 tim |
1977 |
tim |
2102 |
|
1978 |
|
|
* src/io/ZConsWriter.cpp: [no log message] |
1979 |
|
|
|
1980 |
gezelter |
2199 |
2005-01-11 10:53 tim |
1981 |
tim |
2102 |
|
1982 |
|
|
* src/UseTheForce/EAM.cpp: minor fix |
1983 |
|
|
|
1984 |
gezelter |
2199 |
2005-01-11 10:52 tim |
1985 |
tim |
2102 |
|
1986 |
tim |
2116 |
* src/constraints/Rattle.hpp: file Rattle.hpp was initially added |
1987 |
|
|
on branch new_design. |
1988 |
|
|
|
1989 |
gezelter |
2199 |
2005-01-11 10:52 tim |
1990 |
tim |
2116 |
|
1991 |
tim |
2102 |
* src/constraints/Rattle.cpp: file Rattle.cpp was initially added |
1992 |
|
|
on branch new_design. |
1993 |
|
|
|
1994 |
gezelter |
2199 |
2005-01-11 10:52 tim |
1995 |
tim |
2102 |
|
1996 |
|
|
* src/constraints/: Rattle.cpp, Rattle.hpp: adding Rattle Algorithm |
1997 |
|
|
|
1998 |
gezelter |
2199 |
2005-01-11 10:47 tim |
1999 |
tim |
2102 |
|
2000 |
|
|
* make/Makefile.in: forget a '$' sign |
2001 |
|
|
|
2002 |
gezelter |
2199 |
2005-01-11 10:46 tim |
2003 |
tim |
2102 |
|
2004 |
|
|
* make/Makefile.in: missing tab in rules |
2005 |
|
|
|
2006 |
gezelter |
2199 |
2005-01-10 17:04 tim |
2007 |
tim |
2102 |
|
2008 |
|
|
* src/: UseTheForce/ForceFieldCreator.cpp, |
2009 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
2010 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
2011 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
2012 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
2013 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Makefile, |
2014 |
|
|
brains/Register.cpp, brains/Register.hpp, |
2015 |
|
|
integrators/IntegratorCreator.cpp, |
2016 |
|
|
integrators/IntegratorCreator.hpp, |
2017 |
|
|
integrators/IntegratorFactory.cpp, |
2018 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
2019 |
|
|
integrators/NPTi.cpp, integrators/NVE.cpp, integrators/NVT.cpp, |
2020 |
|
|
minimizers/Makefile, minimizers/MinimizerCreator.cpp, |
2021 |
|
|
minimizers/MinimizerCreator.hpp, minimizers/MinimizerFactory.cpp, |
2022 |
|
|
minimizers/MinimizerFactory.hpp: create a register module to |
2023 |
|
|
register force fields, integrators and minimizers |
2024 |
|
|
|
2025 |
gezelter |
2199 |
2005-01-10 17:04 tim |
2026 |
tim |
2102 |
|
2027 |
|
|
* src/brains/Register.cpp: file Register.cpp was initially added on |
2028 |
|
|
branch new_design. |
2029 |
|
|
|
2030 |
gezelter |
2199 |
2005-01-10 17:04 tim |
2031 |
tim |
2102 |
|
2032 |
|
|
* src/brains/Register.hpp: file Register.hpp was initially added on |
2033 |
|
|
branch new_design. |
2034 |
|
|
|
2035 |
gezelter |
2199 |
2005-01-10 15:52 tim |
2036 |
tim |
2102 |
|
2037 |
|
|
* src/: UseTheForce/ForceFieldFactory.cpp, |
2038 |
|
|
applications/oopse/oopse.cpp, brains/ForceManager.hpp, |
2039 |
|
|
constraints/ZconstraintForceManager.cpp, |
2040 |
|
|
constraints/ZconstraintForceManager.hpp, |
2041 |
|
|
integrators/IntegratorFactory.cpp, |
2042 |
|
|
integrators/VelocityVerletIntegrator.cpp, io/ZConsReader.cpp, |
2043 |
|
|
io/ZConsWriter.cpp, minimizers/MinimizerFactory.cpp, |
2044 |
|
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: zconstraint |
2045 |
|
|
method is working now |
2046 |
|
|
|
2047 |
gezelter |
2199 |
2005-01-10 13:05 tim |
2048 |
tim |
2102 |
|
2049 |
|
|
* src/: constraints/ConstraintElem.hpp, |
2050 |
|
|
constraints/ConstraintPair.hpp, constraints/ZconsStruct.hpp, |
2051 |
|
|
constraints/ZconstraintForceManager.cpp, |
2052 |
|
|
constraints/ZconstraintForceManager.hpp, io/ZConsReader.cpp, |
2053 |
|
|
io/ZConsReader.hpp, io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
2054 |
|
|
visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: more work in |
2055 |
|
|
zconstraint |
2056 |
|
|
|
2057 |
gezelter |
2199 |
2005-01-10 13:05 tim |
2058 |
tim |
2102 |
|
2059 |
|
|
* src/constraints/ZconsStruct.hpp: file ZconsStruct.hpp was |
2060 |
|
|
initially added on branch new_design. |
2061 |
|
|
|
2062 |
gezelter |
2199 |
2005-01-07 16:50 tim |
2063 |
tim |
2102 |
|
2064 |
tim |
2116 |
* src/constraints/ZconstraintForceManager.cpp: file |
2065 |
|
|
ZconstraintForceManager.cpp was initially added on branch |
2066 |
|
|
new_design. |
2067 |
|
|
|
2068 |
gezelter |
2199 |
2005-01-07 16:50 tim |
2069 |
tim |
2116 |
|
2070 |
|
|
* src/constraints/ZconstraintForceManager.hpp: file |
2071 |
|
|
ZconstraintForceManager.hpp was initially added on branch |
2072 |
|
|
new_design. |
2073 |
|
|
|
2074 |
gezelter |
2199 |
2005-01-07 16:50 tim |
2075 |
tim |
2116 |
|
2076 |
tim |
2102 |
* src/: applications/simpleBuilder/BaseLattice.hpp, |
2077 |
|
|
applications/simpleBuilder/Lattice.hpp, |
2078 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
2079 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
2080 |
|
|
applications/simpleBuilder/MoLocator.hpp, brains/ForceManager.hpp, |
2081 |
|
|
constraints/ConstraintElem.hpp, constraints/Makefile, |
2082 |
|
|
constraints/ZConstraint.cpp, constraints/ZconsData.hpp, |
2083 |
|
|
constraints/ZconstraintForceManager.cpp, |
2084 |
|
|
constraints/ZconstraintForceManager.hpp, |
2085 |
|
|
integrators/VelocityVerletIntegrator.cpp, primitives/Molecule.hpp, |
2086 |
|
|
utils/NumericConstant.hpp: ZConstraintForceManager in progress |
2087 |
|
|
|
2088 |
gezelter |
2199 |
2005-01-07 16:50 tim |
2089 |
tim |
2102 |
|
2090 |
|
|
* src/constraints/ConstraintElem.hpp: file ConstraintElem.hpp was |
2091 |
|
|
initially added on branch new_design. |
2092 |
|
|
|
2093 |
gezelter |
2199 |
2005-01-06 17:31 tim |
2094 |
tim |
2102 |
|
2095 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
2096 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
2097 |
|
|
constraints/ConstraintPair.hpp, integrators/Integrator.cpp, |
2098 |
|
|
integrators/NPTi.cpp, integrators/VelocityVerletIntegrator.cpp, |
2099 |
|
|
io/Globals.cpp, primitives/Molecule.cpp, primitives/Molecule.hpp: |
2100 |
|
|
constraint is almost working |
2101 |
|
|
|
2102 |
gezelter |
2199 |
2005-01-05 19:36 tim |
2103 |
tim |
2102 |
|
2104 |
|
|
* src/applications/simpleBuilder/MoLocator.cpp: simpleBuilder is |
2105 |
|
|
working |
2106 |
|
|
|
2107 |
gezelter |
2199 |
2005-01-05 19:16 tim |
2108 |
tim |
2102 |
|
2109 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
2110 |
|
|
applications/oopse/oopse.cpp, |
2111 |
|
|
applications/simpleBuilder/BaseLattice.cpp, |
2112 |
|
|
applications/simpleBuilder/Lattice.cpp, |
2113 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
2114 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
2115 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
2116 |
|
|
applications/simpleBuilder/MoLocator.hpp, |
2117 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
2118 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.hpp, |
2119 |
|
|
minimizers/Minimizer.cpp, primitives/RigidBody.cpp: simpleBuilder |
2120 |
|
|
in progress |
2121 |
|
|
|
2122 |
gezelter |
2199 |
2005-01-05 12:35 tim |
2123 |
tim |
2102 |
|
2124 |
|
|
* src/minimizers/MinimizerFactory.hpp: file MinimizerFactory.hpp |
2125 |
|
|
was initially added on branch new_design. |
2126 |
|
|
|
2127 |
gezelter |
2199 |
2005-01-05 12:35 tim |
2128 |
tim |
2102 |
|
2129 |
tim |
2116 |
* src/minimizers/Minimizer.cpp: file Minimizer.cpp was initially |
2130 |
|
|
added on branch new_design. |
2131 |
|
|
|
2132 |
gezelter |
2199 |
2005-01-05 12:35 tim |
2133 |
tim |
2116 |
|
2134 |
tim |
2102 |
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
2135 |
|
|
Makefile, Minimizer.cpp, Minimizer.hpp, MinimizerCreator.cpp, |
2136 |
|
|
MinimizerCreator.hpp, MinimizerFactory.cpp, MinimizerFactory.hpp, |
2137 |
|
|
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, SDMinimizer.cpp, |
2138 |
|
|
SDMinimizer.hpp: minimizer in progress |
2139 |
|
|
|
2140 |
gezelter |
2199 |
2005-01-05 12:35 tim |
2141 |
tim |
2102 |
|
2142 |
tim |
2116 |
* src/minimizers/MinimizerFactory.cpp: file MinimizerFactory.cpp |
2143 |
|
|
was initially added on branch new_design. |
2144 |
tim |
2102 |
|
2145 |
gezelter |
2199 |
2005-01-05 12:35 tim |
2146 |
tim |
2102 |
|
2147 |
tim |
2116 |
* src/minimizers/MinimizerCreator.cpp: file MinimizerCreator.cpp |
2148 |
tim |
2102 |
was initially added on branch new_design. |
2149 |
|
|
|
2150 |
gezelter |
2199 |
2005-01-05 12:35 tim |
2151 |
tim |
2102 |
|
2152 |
tim |
2116 |
* src/minimizers/MinimizerCreator.hpp: file MinimizerCreator.hpp |
2153 |
tim |
2102 |
was initially added on branch new_design. |
2154 |
|
|
|
2155 |
gezelter |
2199 |
2005-01-05 12:35 tim |
2156 |
tim |
2102 |
|
2157 |
|
|
* src/minimizers/Minimizer.hpp: file Minimizer.hpp was initially |
2158 |
|
|
added on branch new_design. |
2159 |
|
|
|
2160 |
gezelter |
2199 |
2005-01-04 17:18 tim |
2161 |
tim |
2102 |
|
2162 |
|
|
* src/: brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
2163 |
|
|
brains/MoleculeCreator.hpp, brains/SimInfo.cpp, brains/Stats.hpp, |
2164 |
|
|
brains/Thermo.cpp, constraints/ConstraintPair.hpp, |
2165 |
|
|
constraints/Makefile, integrators/NPT.cpp, integrators/NVE.cpp, |
2166 |
|
|
integrators/NVT.cpp, integrators/VelocityVerletIntegrator.cpp, |
2167 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpReader.cpp, |
2168 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp: constraints in |
2169 |
|
|
progress |
2170 |
|
|
|
2171 |
gezelter |
2199 |
2005-01-04 17:18 tim |
2172 |
tim |
2102 |
|
2173 |
tim |
2116 |
* src/constraints/ConstraintPair.hpp: file ConstraintPair.hpp was |
2174 |
|
|
initially added on branch new_design. |
2175 |
tim |
2102 |
|
2176 |
gezelter |
2199 |
2005-01-04 17:18 tim |
2177 |
tim |
2102 |
|
2178 |
|
|
* src/minimizers/MinimizerParameterSet.cpp: file |
2179 |
|
|
MinimizerParameterSet.cpp was initially added on branch new_design. |
2180 |
|
|
|
2181 |
gezelter |
2199 |
2005-01-04 17:18 tim |
2182 |
tim |
2102 |
|
2183 |
|
|
* src/minimizers/SDMinimizer.hpp: file SDMinimizer.hpp was |
2184 |
|
|
initially added on branch new_design. |
2185 |
|
|
|
2186 |
gezelter |
2199 |
2005-01-04 17:18 tim |
2187 |
tim |
2102 |
|
2188 |
tim |
2116 |
* src/minimizers/CGFamilyMinimizer.hpp: file CGFamilyMinimizer.hpp |
2189 |
|
|
was initially added on branch new_design. |
2190 |
|
|
|
2191 |
gezelter |
2199 |
2005-01-04 17:18 tim |
2192 |
tim |
2116 |
|
2193 |
|
|
* src/minimizers/: CGFamilyMinimizer.cpp, CGFamilyMinimizer.hpp, |
2194 |
|
|
Makefile, MinimizerParameterSet.cpp, MinimizerParameterSet.hpp, |
2195 |
|
|
OOPSEMinimizer.cpp, OOPSEMinimizer.hpp, PRCG.cpp, PRCG.hpp, |
2196 |
|
|
SDMinimizer.cpp, SDMinimizer.hpp: minimizers in progress |
2197 |
|
|
|
2198 |
gezelter |
2199 |
2005-01-04 17:18 tim |
2199 |
tim |
2116 |
|
2200 |
tim |
2102 |
* src/minimizers/PRCG.hpp: file PRCG.hpp was initially added on |
2201 |
|
|
branch new_design. |
2202 |
|
|
|
2203 |
gezelter |
2199 |
2004-12-20 15:50 chuckv |
2204 |
tim |
2102 |
|
2205 |
|
|
* make/Makefile.in: Fixed Makefile test bug under OSX and possibly |
2206 |
|
|
other BSD's, replaced test -f *.mod with ls function since BSD test |
2207 |
|
|
apparently doesn't support wildcards. |
2208 |
|
|
|
2209 |
gezelter |
2199 |
2004-12-20 15:36 tim |
2210 |
tim |
2102 |
|
2211 |
|
|
* make/Makefile.in: fix a test command incompatiable problem |
2212 |
|
|
|
2213 |
gezelter |
2199 |
2004-12-20 14:49 tim |
2214 |
tim |
2102 |
|
2215 |
|
|
* src/integrators/NPTi.cpp: NPT is working now |
2216 |
|
|
|
2217 |
gezelter |
2199 |
2004-12-16 14:20 tim |
2218 |
tim |
2102 |
|
2219 |
|
|
* src/brains/SimInfo.cpp: Fix a bug in SimInfo which gives the |
2220 |
|
|
invalid stamp id |
2221 |
|
|
|
2222 |
gezelter |
2199 |
2004-12-16 14:00 tim |
2223 |
tim |
2102 |
|
2224 |
|
|
* forceFields/: newEAM.VC.frc, newEAM.frc, newEAM.u3.frc, |
2225 |
|
|
newEAM.u6.frc: adding new EAM force field files |
2226 |
|
|
|
2227 |
gezelter |
2199 |
2004-12-16 13:55 tim |
2228 |
tim |
2102 |
|
2229 |
|
|
* src/io/EAMAtomTypesSectionParser.cpp: parsing order three arrays |
2230 |
|
|
in EAM parameter file is incorrect |
2231 |
|
|
|
2232 |
gezelter |
2199 |
2004-12-16 12:27 tim |
2233 |
tim |
2102 |
|
2234 |
|
|
* src/: UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, |
2235 |
|
|
brains/SimCreator.cpp, io/EAMAtomTypesSectionParser.cpp, |
2236 |
|
|
utils/StringTokenizer.cpp: add getMaxRcutFromAtomType into EAM |
2237 |
|
|
|
2238 |
gezelter |
2199 |
2004-12-15 17:34 tim |
2239 |
tim |
2102 |
|
2240 |
|
|
* src/: applications/simpleBuilder/BaseLattice.cpp, |
2241 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
2242 |
|
|
applications/simpleBuilder/Lattice.cpp, |
2243 |
|
|
applications/simpleBuilder/Lattice.hpp, |
2244 |
|
|
applications/simpleBuilder/LatticeCreator.cpp, |
2245 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
2246 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
2247 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
2248 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
2249 |
|
|
io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream |
2250 |
|
|
|
2251 |
gezelter |
2199 |
2004-12-15 16:07 tim |
2252 |
tim |
2102 |
|
2253 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2254 |
|
|
UseTheForce/EAM.cpp, UseTheForce/EAM.hpp, UseTheForce/Makefile, |
2255 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp: |
2256 |
|
|
add EAM Force Field |
2257 |
|
|
|
2258 |
gezelter |
2199 |
2004-12-15 14:40 tim |
2259 |
tim |
2102 |
|
2260 |
|
|
* src/applications/oopse/oopse.cpp: add more force fields |
2261 |
|
|
|
2262 |
gezelter |
2199 |
2004-12-15 11:44 tim |
2263 |
tim |
2102 |
|
2264 |
|
|
* src/brains/SimInfo.cpp: fix bugs in getCom and getComVel (forget |
2265 |
|
|
to call All_reduce in MPI version) |
2266 |
|
|
|
2267 |
gezelter |
2199 |
2004-12-15 11:13 tim |
2268 |
tim |
2102 |
|
2269 |
|
|
* src/: brains/SimCreator.cpp, brains/SimInfo.cpp, |
2270 |
|
|
io/DumpReader.cpp: MPI in NVE is working |
2271 |
|
|
|
2272 |
gezelter |
2199 |
2004-12-14 16:57 tim |
2273 |
tim |
2102 |
|
2274 |
|
|
* src/io/: DumpReader.cpp, DumpReader.hpp: fix a bug in DumpReader. |
2275 |
|
|
Master nodes does not brocast the total number of frames |
2276 |
|
|
|
2277 |
gezelter |
2199 |
2004-12-14 14:08 tim |
2278 |
tim |
2102 |
|
2279 |
|
|
* src/: brains/SimCreator.cpp, brains/SimSnapshotManager.hpp, |
2280 |
|
|
integrators/NVE.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
2281 |
|
|
minimizers/CGFamilyMinimizer.cpp, |
2282 |
|
|
minimizers/MinimizerParameterSet.hpp, |
2283 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
2284 |
|
|
minimizers/SDMinimizer.cpp: more fix in MPI version |
2285 |
|
|
|
2286 |
gezelter |
2199 |
2004-12-13 17:30 tim |
2287 |
tim |
2102 |
|
2288 |
|
|
* src/: UseTheForce/DarkSide/simParallel.F90, |
2289 |
|
|
applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
2290 |
|
|
brains/SimInfo.cpp, brains/Snapshot.hpp, brains/Thermo.cpp, |
2291 |
|
|
integrators/DLM.cpp, integrators/Integrator.cpp, |
2292 |
|
|
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
2293 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp, io/DumpReader.cpp, |
2294 |
|
|
io/DumpWriter.cpp, io/EAMAtomTypesSectionParser.cpp, |
2295 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, io/SectionParser.hpp, |
2296 |
|
|
io/ZConsWriter.cpp, io/ZConsWriter.hpp, io/basic_ifstrstream.hpp, |
2297 |
|
|
math/SquareMatrix3.hpp, primitives/Bend.hpp, primitives/Bond.hpp, |
2298 |
|
|
primitives/RigidBody.cpp, primitives/StuntDouble.cpp, |
2299 |
|
|
primitives/StuntDouble.hpp, types/CutoffGroupStamp.cpp, |
2300 |
|
|
utils/LocalIndexManager.hpp, utils/PropertyMap.cpp, |
2301 |
|
|
utils/PropertyMap.hpp, visitors/CompositeVisitor.cpp: MPI version |
2302 |
|
|
is built |
2303 |
|
|
|
2304 |
gezelter |
2199 |
2004-12-10 13:41 tim |
2305 |
tim |
2102 |
|
2306 |
|
|
* src/UseTheForce/WATER.cpp: fix another bug in WATER.cpp |
2307 |
|
|
|
2308 |
gezelter |
2199 |
2004-12-10 11:14 tim |
2309 |
tim |
2102 |
|
2310 |
|
|
* src/: brains/ForceManager.cpp, primitives/StuntDouble.cpp, |
2311 |
|
|
primitives/StuntDouble.hpp: forget to zero out the torque. Sticky |
2312 |
|
|
and Dipole is working now |
2313 |
|
|
|
2314 |
gezelter |
2199 |
2004-12-09 18:15 tim |
2315 |
tim |
2102 |
|
2316 |
|
|
* src/: UseTheForce/DarkSide/dipole.F90, |
2317 |
|
|
UseTheForce/DarkSide/reactionField.F90, primitives/StuntDouble.hpp: |
2318 |
|
|
fix an index problem in eFrame matrix |
2319 |
|
|
|
2320 |
gezelter |
2199 |
2004-12-09 18:09 tim |
2321 |
tim |
2102 |
|
2322 |
|
|
* src/UseTheForce/WATER.cpp: fix a bug in WATER.cpp when |
2323 |
|
|
initializing the new Charge AtomType |
2324 |
|
|
|
2325 |
gezelter |
2199 |
2004-12-09 16:15 tim |
2326 |
tim |
2102 |
|
2327 |
|
|
* src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/sticky.F90, |
2328 |
|
|
types/DirectionalAtomType.cpp: sticky module get compiled |
2329 |
|
|
|
2330 |
gezelter |
2199 |
2004-12-09 15:43 gezelter |
2331 |
tim |
2102 |
|
2332 |
|
|
* src/UseTheForce/DarkSide/: dipole.F90, force_globals.F90, gb.F90, |
2333 |
|
|
reactionField.F90: u_l -> eFrame for electrostatics u_l -> A for |
2334 |
|
|
GB |
2335 |
|
|
|
2336 |
gezelter |
2199 |
2004-12-09 15:42 gezelter |
2337 |
tim |
2102 |
|
2338 |
|
|
* src/UseTheForce/doForces.F90: u_l -> eFrame |
2339 |
|
|
|
2340 |
gezelter |
2199 |
2004-12-09 15:27 gezelter |
2341 |
tim |
2102 |
|
2342 |
|
|
* src/UseTheForce/DarkSide/: sticky.F90, sticky_interface.h: sticky |
2343 |
|
|
module now has the option for multiple sticky types |
2344 |
|
|
|
2345 |
gezelter |
2199 |
2004-12-09 15:27 gezelter |
2346 |
tim |
2102 |
|
2347 |
|
|
* src/UseTheForce/doForces.F90: sticky |
2348 |
|
|
|
2349 |
gezelter |
2199 |
2004-12-09 11:22 tim |
2350 |
tim |
2102 |
|
2351 |
|
|
* src/integrators/: NPT.cpp, NVT.cpp: fix an interface |
2352 |
|
|
inconsistency in lab2Bidy |
2353 |
|
|
|
2354 |
gezelter |
2199 |
2004-12-09 10:45 tim |
2355 |
tim |
2102 |
|
2356 |
|
|
* src/: math/SquareMatrix3.hpp, primitives/RigidBody.cpp: Fix a bug |
2357 |
|
|
in calculating torque in rigid body |
2358 |
|
|
|
2359 |
gezelter |
2199 |
2004-12-08 15:37 tim |
2360 |
tim |
2102 |
|
2361 |
|
|
* src/: UseTheForce/mpiForceField.c, UseTheForce/mpiForceField.h, |
2362 |
|
|
brains/SnapShot.cpp, brains/Snapshot.hpp, |
2363 |
|
|
integrators/Integrator.cpp, |
2364 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, utils/MemoryUtils.hpp: |
2365 |
|
|
fix a parsing bug in ElectroStaticAtomTypesSectionParser |
2366 |
|
|
|
2367 |
gezelter |
2199 |
2004-12-08 12:03 tim |
2368 |
tim |
2102 |
|
2369 |
|
|
* src/integrators/: NVT.cpp, VelocityVerletIntegrator.cpp: Butane |
2370 |
|
|
in NVT is working |
2371 |
|
|
|
2372 |
gezelter |
2199 |
2004-12-07 18:08 tim |
2373 |
tim |
2102 |
|
2374 |
|
|
* src/: UseTheForce/Makefile, brains/SimInfo.hpp, |
2375 |
|
|
integrators/NPT.cpp, integrators/NPTf.cpp, integrators/NPTi.cpp, |
2376 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp, integrators/NVT.hpp, |
2377 |
|
|
io/DumpWriter.cpp: NPT in progress |
2378 |
|
|
|
2379 |
gezelter |
2199 |
2004-12-07 09:43 tim |
2380 |
tim |
2102 |
|
2381 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.hpp: [no log |
2382 |
|
|
message] |
2383 |
|
|
|
2384 |
gezelter |
2199 |
2004-12-07 00:12 tim |
2385 |
tim |
2102 |
|
2386 |
|
|
* src/integrators/: Integrator.cpp, NPT.cpp, NPTi.cpp: fix a bug in |
2387 |
|
|
UseInitXSstate |
2388 |
|
|
|
2389 |
gezelter |
2199 |
2004-12-07 00:00 tim |
2390 |
tim |
2102 |
|
2391 |
|
|
* src/: io/DumpReader.cpp, utils/StringTokenizer.hpp: no message |
2392 |
|
|
|
2393 |
gezelter |
2199 |
2004-12-06 23:47 tim |
2394 |
tim |
2102 |
|
2395 |
|
|
* src/types/DirectionalAtomType.cpp: [no log message] |
2396 |
|
|
|
2397 |
gezelter |
2199 |
2004-12-06 21:18 tim |
2398 |
tim |
2102 |
|
2399 |
|
|
* forceFields/newDUFF.frc: merge WATER force field into DUFF |
2400 |
|
|
|
2401 |
gezelter |
2199 |
2004-12-06 20:33 tim |
2402 |
tim |
2102 |
|
2403 |
|
|
* forceFields/newDUFF.frc: change the force constant of bonds |
2404 |
|
|
|
2405 |
gezelter |
2199 |
2004-12-06 18:29 tim |
2406 |
tim |
2102 |
|
2407 |
|
|
* src/: UseTheForce/DarkSide/charge.F90, |
2408 |
|
|
UseTheForce/DarkSide/charge_interface.h, |
2409 |
|
|
UseTheForce/DarkSide/dipole.F90, |
2410 |
|
|
UseTheForce/DarkSide/dipole_interface.h, primitives/Torsion.cpp: |
2411 |
|
|
fix atom type ident in Charge and Dipole Module |
2412 |
|
|
|
2413 |
gezelter |
2199 |
2004-12-06 17:56 tim |
2414 |
tim |
2102 |
|
2415 |
|
|
* src/primitives/Torsion.cpp: butane is working now |
2416 |
|
|
|
2417 |
gezelter |
2199 |
2004-12-06 15:15 tim |
2418 |
tim |
2102 |
|
2419 |
|
|
* src/: brains/MoleculeCreator.cpp, primitives/Bend.cpp, |
2420 |
|
|
primitives/Bond.hpp, primitives/Torsion.cpp: short range |
2421 |
|
|
interaction for butane is correct.Still something wrong with long |
2422 |
|
|
range one |
2423 |
|
|
|
2424 |
gezelter |
2199 |
2004-12-05 23:49 tim |
2425 |
tim |
2102 |
|
2426 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
2427 |
|
|
brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
2428 |
|
|
io/BendTypesSectionParser.cpp, math/Polynomial.hpp, |
2429 |
|
|
primitives/Atom.hpp, utils/NumericConstant.hpp, |
2430 |
|
|
utils/TypeContainer.hpp: fix a bug in Exclude List |
2431 |
|
|
|
2432 |
gezelter |
2199 |
2004-12-05 17:21 tim |
2433 |
tim |
2102 |
|
2434 |
|
|
* forceFields/newDUFF.frc: minor fix in DUFF |
2435 |
|
|
|
2436 |
gezelter |
2199 |
2004-12-05 17:02 tim |
2437 |
tim |
2102 |
|
2438 |
|
|
* src/: brains/SimInfo.cpp, brains/Thermo.cpp, math/Vector.hpp, |
2439 |
|
|
utils/StringTokenizer.cpp, utils/Utility.cpp, utils/Utility.hpp: |
2440 |
|
|
fix a bug in filling MolMembership |
2441 |
|
|
|
2442 |
gezelter |
2199 |
2004-12-05 12:12 tim |
2443 |
tim |
2102 |
|
2444 |
|
|
* forceFields/newDUFF.frc: minor fix in force field file |
2445 |
|
|
|
2446 |
gezelter |
2199 |
2004-12-05 12:09 tim |
2447 |
tim |
2102 |
|
2448 |
|
|
* src/: applications/oopse/oopse.cpp, integrators/Integrator.cpp, |
2449 |
|
|
integrators/NPTxyz.cpp, integrators/NVT.cpp: add Integrator.cpp |
2450 |
|
|
|
2451 |
gezelter |
2199 |
2004-12-04 15:09 tim |
2452 |
tim |
2102 |
|
2453 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, math/Polynomial.hpp, |
2454 |
|
|
math/Vector3.hpp: NVE is working now, get the same result as |
2455 |
|
|
OOPSE-1.0 |
2456 |
|
|
|
2457 |
gezelter |
2199 |
2004-12-04 14:29 tim |
2458 |
tim |
2102 |
|
2459 |
|
|
* src/primitives/: Bend.cpp, Torsion.cpp: rewind to old copy |
2460 |
|
|
|
2461 |
gezelter |
2199 |
2004-12-04 14:24 gezelter |
2462 |
tim |
2102 |
|
2463 |
|
|
* src/primitives/: Bend.cpp, Torsion.cpp: What? |
2464 |
|
|
|
2465 |
gezelter |
2199 |
2004-12-04 14:24 gezelter |
2466 |
tim |
2102 |
|
2467 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: atid / c_ident confusion |
2468 |
|
|
|
2469 |
gezelter |
2199 |
2004-12-04 00:24 tim |
2470 |
tim |
2102 |
|
2471 |
|
|
* src/: UseTheForce/ForceField.cpp, brains/Thermo.cpp, |
2472 |
|
|
integrators/Integrator.hpp, |
2473 |
|
|
integrators/VelocityVerletIntegrator.cpp, primitives/Torsion.cpp, |
2474 |
|
|
utils/TypeContainer.hpp: NVE conserved energy, however, potential |
2475 |
|
|
is not the same as OOPSE-1.0 Step 1 argon in NVE, NVT, NPTi, NPTf |
2476 |
|
|
and NPTxyz to test integrator Step 2 SSD in NVE to test DLM, |
2477 |
|
|
dipole, sticky Step 3 Butane in NVE to test Bond Bend Torsion Step |
2478 |
|
|
4 EAM Step 5 Shape Step 6 Constraint & Restraint |
2479 |
|
|
|
2480 |
gezelter |
2199 |
2004-12-03 19:01 tim |
2481 |
tim |
2102 |
|
2482 |
|
|
* src/: UseTheForce/DarkSide/LJ.F90, |
2483 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, brains/DataStorage.cpp, |
2484 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
2485 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
2486 |
|
|
io/StatWriter.hpp, primitives/Atom.cpp: Dump2Xyz is also working, |
2487 |
|
|
energy of NVE is not conserved |
2488 |
|
|
|
2489 |
gezelter |
2199 |
2004-12-03 17:36 tim |
2490 |
tim |
2102 |
|
2491 |
|
|
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
2492 |
|
|
primitives/Molecule.cpp, primitives/StuntDouble.hpp: NVE is running |
2493 |
|
|
|
2494 |
gezelter |
2199 |
2004-12-03 16:30 tim |
2495 |
tim |
2102 |
|
2496 |
|
|
* src/: applications/oopse/oopse.cpp, brains/SimInfo.cpp, |
2497 |
|
|
brains/SimInfo.hpp, brains/Thermo.hpp, integrators/Makefile, |
2498 |
|
|
integrators/NVE.cpp, primitives/Molecule.cpp, |
2499 |
|
|
primitives/Molecule.hpp, primitives/StuntDouble.hpp, |
2500 |
|
|
primitives/Torsion.hpp: more missing function get implemented |
2501 |
|
|
|
2502 |
gezelter |
2199 |
2004-12-03 15:30 tim |
2503 |
tim |
2102 |
|
2504 |
|
|
* src/brains/: MoleculeCreator.cpp, SimCreator.cpp, SimCreator.hpp, |
2505 |
|
|
SimInfo.cpp, SimInfo.hpp: Change interface of SimInfo |
2506 |
|
|
|
2507 |
gezelter |
2199 |
2004-12-03 12:59 tim |
2508 |
tim |
2102 |
|
2509 |
|
|
* src/: applications/oopse/oopse.cpp, brains/SimCreator.cpp, |
2510 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
2511 |
|
|
integrators/NPT.cpp, integrators/NPTi.cpp, integrators/NVT.cpp, |
2512 |
|
|
io/BASS_interface.cpp, io/DirectionalAtomTypesSectionParser.cpp, |
2513 |
|
|
io/SectionParserManager.cpp, utils/LocalIndexManager.hpp, |
2514 |
|
|
utils/TypeContainer.hpp: begin to fix bugs |
2515 |
|
|
|
2516 |
gezelter |
2199 |
2004-12-02 19:26 tim |
2517 |
tim |
2102 |
|
2518 |
tim |
2116 |
* src/utils/Trim.cpp: file Trim.cpp was initially added on branch |
2519 |
|
|
new_design. |
2520 |
|
|
|
2521 |
gezelter |
2199 |
2004-12-02 19:26 tim |
2522 |
tim |
2116 |
|
2523 |
tim |
2102 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2524 |
|
|
UseTheForce/ForceFieldCreator.cpp, |
2525 |
|
|
UseTheForce/ForceFieldFactory.cpp, applications/oopse/oopse.cpp, |
2526 |
|
|
integrators/IntegratorCreator.cpp, |
2527 |
|
|
integrators/IntegratorFactory.cpp, io/SectionParserManager.cpp, |
2528 |
|
|
io/SectionParserManager.hpp, utils/Makefile, |
2529 |
|
|
utils/StringTokenizer.cpp, utils/Trim.cpp, utils/Trim.hpp: Fixed a |
2530 |
|
|
bug in countTokens in StringTokenizer |
2531 |
|
|
|
2532 |
gezelter |
2199 |
2004-12-02 19:06 tim |
2533 |
tim |
2102 |
|
2534 |
|
|
* forceFields/newDUFF.frc: minor fix |
2535 |
|
|
|
2536 |
gezelter |
2199 |
2004-12-02 18:15 tim |
2537 |
tim |
2102 |
|
2538 |
|
|
* forceFields/newDUFF.frc: new ForceField format |
2539 |
|
|
|
2540 |
gezelter |
2199 |
2004-12-02 17:15 tim |
2541 |
tim |
2102 |
|
2542 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2543 |
|
|
UseTheForce/ForceFieldCreator.cpp, |
2544 |
|
|
UseTheForce/ForceFieldCreator.hpp, |
2545 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
2546 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/Makefile, |
2547 |
|
|
applications/oopse/oopse.cpp, integrators/IntegratorCreator.cpp, |
2548 |
|
|
integrators/IntegratorCreator.hpp, |
2549 |
|
|
integrators/IntegratorFactory.cpp, |
2550 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
2551 |
|
|
integrators/NPTf.cpp, integrators/NPTf.hpp, integrators/NPTi.cpp, |
2552 |
|
|
integrators/NPTi.hpp, integrators/NPTxyz.cpp, |
2553 |
|
|
integrators/NPTxyz.hpp, integrators/NVE.cpp, integrators/NVE.hpp, |
2554 |
|
|
integrators/NVT.cpp, integrators/NVT.hpp, |
2555 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
2556 |
|
|
types/Makefile: refine factory pattern to make it initialized |
2557 |
|
|
correctly |
2558 |
|
|
|
2559 |
gezelter |
2199 |
2004-12-02 17:15 tim |
2560 |
tim |
2102 |
|
2561 |
|
|
* src/UseTheForce/ForceFieldCreator.hpp: file ForceFieldCreator.hpp |
2562 |
|
|
was initially added on branch new_design. |
2563 |
|
|
|
2564 |
gezelter |
2199 |
2004-12-02 17:15 tim |
2565 |
tim |
2102 |
|
2566 |
tim |
2116 |
* src/UseTheForce/ForceFieldCreator.cpp: file ForceFieldCreator.cpp |
2567 |
|
|
was initially added on branch new_design. |
2568 |
|
|
|
2569 |
gezelter |
2199 |
2004-12-02 17:15 tim |
2570 |
tim |
2116 |
|
2571 |
|
|
* src/integrators/IntegratorCreator.cpp: file IntegratorCreator.cpp |
2572 |
|
|
was initially added on branch new_design. |
2573 |
|
|
|
2574 |
gezelter |
2199 |
2004-12-02 17:15 tim |
2575 |
tim |
2116 |
|
2576 |
|
|
* src/integrators/IntegratorCreator.hpp: file IntegratorCreator.hpp |
2577 |
|
|
was initially added on branch new_design. |
2578 |
|
|
|
2579 |
gezelter |
2199 |
2004-12-02 11:53 tim |
2580 |
tim |
2116 |
|
2581 |
tim |
2102 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, brains/Stats.cpp, |
2582 |
|
|
types/DirectionalAtomType.cpp, types/Makefile: oopse get built |
2583 |
|
|
|
2584 |
gezelter |
2199 |
2004-12-02 11:04 tim |
2585 |
tim |
2102 |
|
2586 |
|
|
* src/: applications/simpleBuilder/LatticeCreator.cpp, |
2587 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
2588 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
2589 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
2590 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Exclude.cpp, |
2591 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
2592 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, |
2593 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
2594 |
|
|
brains/SnapshotManager.hpp, brains/Stats.cpp, |
2595 |
|
|
constraints/ZconsData.hpp, io/DumpWriter.cpp, io/LinkedAssign.hpp, |
2596 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.hpp, |
2597 |
|
|
io/basic_ifstrstream.hpp, primitives/Bend.hpp, |
2598 |
|
|
primitives/GhostBend.cpp, primitives/GhostBend.hpp, |
2599 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
2600 |
|
|
types/OplsTorsionType.hpp, types/ShapeAtomType.hpp, |
2601 |
|
|
utils/PropertyMap.hpp, utils/TypeContainer.hpp, |
2602 |
|
|
visitors/AtomVisitor.cpp, visitors/CompositeVisitor.cpp, |
2603 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
2604 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
2605 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: still |
2606 |
|
|
have two linking problem |
2607 |
|
|
|
2608 |
gezelter |
2199 |
2004-12-02 00:17 tim |
2609 |
tim |
2102 |
|
2610 |
|
|
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
2611 |
|
|
applications/simpleBuilder/Lattice.cpp, |
2612 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
2613 |
|
|
constraints/ZConstraint.cpp, io/DumpWriter.cpp, io/ZConsReader.cpp, |
2614 |
|
|
io/ZConsWriter.cpp, minimizers/CGFamilyMinimizer.cpp, |
2615 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/SDMinimizer.cpp, |
2616 |
|
|
restraints/Restraints.cpp, visitors/AtomVisitor.cpp, |
2617 |
|
|
visitors/OtherVisitor.cpp, visitors/RigidBodyVisitor.cpp, |
2618 |
|
|
visitors/ZconsVisitor.cpp: change endl to std::endl |
2619 |
|
|
|
2620 |
gezelter |
2199 |
2004-12-02 00:14 tim |
2621 |
tim |
2102 |
|
2622 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
2623 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
2624 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
2625 |
|
|
applications/simpleBuilder/Lattice.hpp, |
2626 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
2627 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
2628 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
2629 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
2630 |
|
|
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
2631 |
|
|
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
2632 |
|
|
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
2633 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
2634 |
|
|
visitors/RigidBodyVisitor.hpp: minor fix |
2635 |
|
|
|
2636 |
gezelter |
2199 |
2004-12-02 00:09 tim |
2637 |
tim |
2102 |
|
2638 |
|
|
* src/utils/: Makefile, StreamTokenizer.cpp, StreamTokenizer.hpp: |
2639 |
|
|
remove StreamTokenizer |
2640 |
|
|
|
2641 |
gezelter |
2199 |
2004-12-02 00:06 tim |
2642 |
tim |
2102 |
|
2643 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
2644 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, applications/oopse/oopse.cpp, |
2645 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, brains/Thermo.cpp, |
2646 |
|
|
io/ZConsWriter.cpp, math/randomSPRNG.cpp, |
2647 |
|
|
restraints/Restraints.cpp, utils/StreamTokenizer.cpp: remove using |
2648 |
|
|
namespace std in .cpp file |
2649 |
|
|
|
2650 |
gezelter |
2199 |
2004-12-02 00:04 tim |
2651 |
tim |
2102 |
|
2652 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
2653 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
2654 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
2655 |
|
|
applications/simpleBuilder/Lattice.cpp, |
2656 |
|
|
applications/simpleBuilder/Lattice.hpp, |
2657 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
2658 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
2659 |
|
|
applications/simpleBuilder/MoLocator.cpp, |
2660 |
|
|
applications/simpleBuilder/MoLocator.hpp, brains/SkipList.cpp, |
2661 |
|
|
brains/SkipList.hpp, constraints/ZconsData.hpp, io/ZConsReader.cpp, |
2662 |
|
|
io/ZConsWriter.cpp, io/ZConsWriter.hpp, |
2663 |
|
|
minimizers/MinimizerParameterSet.hpp, |
2664 |
|
|
minimizers/OOPSEMinimizer.cpp, minimizers/OOPSEMinimizer.hpp, |
2665 |
|
|
minimizers/PRCG.cpp, primitives/Atom.cpp, primitives/RigidBody.cpp, |
2666 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp, |
2667 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
2668 |
|
|
types/ShapeAtomType.cpp, types/ShapeAtomType.hpp, |
2669 |
|
|
utils/GenericData.hpp, visitors/CompositeVisitor.cpp, |
2670 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
2671 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp: adding |
2672 |
|
|
qulified name prefix std |
2673 |
|
|
|
2674 |
gezelter |
2199 |
2004-12-01 23:55 tim |
2675 |
tim |
2102 |
|
2676 |
|
|
* src/: UseTheForce/Shapes_FF.cpp, |
2677 |
|
|
applications/dump2Xyz/Dump2XYZ.cpp, |
2678 |
|
|
applications/simpleBuilder/BaseLattice.hpp, |
2679 |
|
|
applications/simpleBuilder/Lattice.hpp, |
2680 |
|
|
applications/simpleBuilder/LatticeCreator.hpp, |
2681 |
|
|
applications/simpleBuilder/LatticeFactory.cpp, |
2682 |
|
|
applications/simpleBuilder/LatticeFactory.hpp, |
2683 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, io/DumpWriter.cpp, |
2684 |
|
|
io/LinkedAssign.hpp, io/basic_ifstrstream.hpp, |
2685 |
|
|
minimizers/OOPSEMinimizer.hpp, utils/GenericData.hpp, |
2686 |
|
|
utils/GenericFactory.hpp, visitors/CompositeVisitor.cpp, |
2687 |
|
|
visitors/CompositeVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
2688 |
|
|
visitors/RigidBodyVisitor.hpp: replace string by std::string |
2689 |
|
|
|
2690 |
gezelter |
2199 |
2004-12-01 22:12 tim |
2691 |
tim |
2102 |
|
2692 |
|
|
* make/Makefile.in, src/UseTheForce/ForceFieldFactory.hpp, |
2693 |
|
|
src/applications/simpleBuilder/BaseLattice.hpp, |
2694 |
|
|
src/applications/simpleBuilder/Lattice.hpp, |
2695 |
|
|
src/applications/simpleBuilder/LatticeCreator.hpp, |
2696 |
|
|
src/applications/simpleBuilder/LatticeFactory.hpp, |
2697 |
|
|
src/applications/simpleBuilder/MoLocator.hpp, |
2698 |
|
|
src/brains/SimInfo.cpp, src/brains/SkipList.hpp, |
2699 |
|
|
src/brains/Snapshot.hpp, src/constraints/ZconsData.hpp, |
2700 |
|
|
src/integrators/IntegratorFactory.hpp, src/io/Globals.hpp, |
2701 |
|
|
src/io/ZConsWriter.hpp, src/io/basic_ifstrstream.hpp, |
2702 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/primitives/StuntDouble.hpp, |
2703 |
|
|
src/types/MoleculeStamp.hpp, src/types/ShapeAtomType.hpp, |
2704 |
|
|
src/utils/Makefile, src/utils/StringUtils.cpp, |
2705 |
|
|
src/utils/StringUtils.hpp, src/utils/TypeInfo.hpp, |
2706 |
|
|
src/utils/Utility.cpp, src/visitors/CompositeVisitor.hpp, |
2707 |
|
|
src/visitors/RigidBodyVisitor.hpp, test/brains/DirectionalAtom.cpp, |
2708 |
|
|
test/brains/RigidBody.cpp: replace misuse of using namespace std in |
2709 |
|
|
header files |
2710 |
|
|
|
2711 |
gezelter |
2199 |
2004-12-01 21:23 tim |
2712 |
tim |
2102 |
|
2713 |
|
|
* src/: primitives/Atom.hpp, primitives/RigidBody.hpp, |
2714 |
|
|
primitives/StuntDouble.hpp, utils/TypeContainer.hpp, |
2715 |
|
|
utils/Utility.cpp, utils/Utility.hpp, utils/next_combination.hpp: |
2716 |
|
|
begin to fix linking problem |
2717 |
|
|
|
2718 |
gezelter |
2199 |
2004-12-01 21:08 tim |
2719 |
tim |
2102 |
|
2720 |
|
|
* src/: applications/oopse/oopse.cpp, brains/Stats.cpp, |
2721 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, integrators/Makefile, |
2722 |
|
|
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
2723 |
|
|
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
2724 |
|
|
integrators/NPTxyz.cpp, integrators/VelocityVerletIntegrator.hpp, |
2725 |
|
|
math/SquareMatrix3.hpp, primitives/Atom.hpp, |
2726 |
|
|
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
2727 |
|
|
utils/OOPSEConstant.hpp, utils/StringUtils.cpp: oopse get compiled, |
2728 |
|
|
still has some linking problem |
2729 |
|
|
|
2730 |
gezelter |
2199 |
2004-12-01 19:26 tim |
2731 |
tim |
2102 |
|
2732 |
|
|
* src/: integrators/NVT.cpp, integrators/NVT.hpp, |
2733 |
|
|
utils/OOPSEConstant.hpp: NVT get built |
2734 |
|
|
|
2735 |
gezelter |
2199 |
2004-12-01 19:09 tim |
2736 |
tim |
2102 |
|
2737 |
tim |
2116 |
* src/integrators/DLM.cpp: file DLM.cpp was initially added on |
2738 |
|
|
branch new_design. |
2739 |
tim |
2102 |
|
2740 |
gezelter |
2199 |
2004-12-01 19:09 tim |
2741 |
tim |
2102 |
|
2742 |
tim |
2116 |
* src/integrators/DLM.hpp: file DLM.hpp was initially added on |
2743 |
|
|
branch new_design. |
2744 |
|
|
|
2745 |
gezelter |
2199 |
2004-12-01 19:09 tim |
2746 |
tim |
2116 |
|
2747 |
tim |
2102 |
* src/: brains/SimSnapshotManager.cpp, brains/Snapshot.hpp, |
2748 |
|
|
brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp, |
2749 |
|
|
brains/Thermo.hpp, integrators/DLM.cpp, integrators/DLM.hpp, |
2750 |
|
|
integrators/Integrator.hpp, integrators/Makefile, |
2751 |
|
|
integrators/NVE.cpp, integrators/NVE.hpp, |
2752 |
|
|
integrators/RotationAlgorithm.hpp, |
2753 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
2754 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWriter.hpp: NVE |
2755 |
|
|
get built |
2756 |
|
|
|
2757 |
gezelter |
2199 |
2004-12-01 19:09 tim |
2758 |
tim |
2102 |
|
2759 |
tim |
2116 |
* src/integrators/RotationAlgorithm.hpp: file RotationAlgorithm.hpp |
2760 |
|
|
was initially added on branch new_design. |
2761 |
tim |
2102 |
|
2762 |
gezelter |
2199 |
2004-12-01 17:45 tim |
2763 |
tim |
2102 |
|
2764 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, integrators/Integrator.hpp, |
2765 |
|
|
integrators/IntegratorFactory.cpp, |
2766 |
|
|
integrators/IntegratorFactory.hpp, integrators/Makefile, |
2767 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
2768 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
2769 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/DumpWrite.hpp, |
2770 |
|
|
io/DumpWriter.cpp, io/DumpWriter.hpp, io/StatWriter.cpp, |
2771 |
|
|
io/StatWriter.hpp: rename DumpWrite to DumpWriter |
2772 |
|
|
|
2773 |
gezelter |
2199 |
2004-12-01 17:45 tim |
2774 |
tim |
2102 |
|
2775 |
|
|
* src/io/DumpWriter.hpp: file DumpWriter.hpp was initially added on |
2776 |
|
|
branch new_design. |
2777 |
|
|
|
2778 |
gezelter |
2199 |
2004-12-01 15:05 tim |
2779 |
tim |
2102 |
|
2780 |
|
|
* src/: io/Makefile, io/ZConsReader.cpp, io/ZConsReader.hpp, |
2781 |
|
|
io/ZConsWriter.hpp, math/Vector3.hpp, utils/Makefile, |
2782 |
|
|
utils/Utility.cpp, utils/Utility.hpp, visitors/AtomData.hpp, |
2783 |
|
|
visitors/BaseVisitor.hpp, visitors/OtherVisitor.cpp, |
2784 |
|
|
visitors/OtherVisitor.hpp, visitors/ZconsVisitor.cpp, |
2785 |
|
|
visitors/ZconsVisitor.hpp: visitors get built |
2786 |
|
|
|
2787 |
gezelter |
2199 |
2004-12-01 14:32 chrisfen |
2788 |
tim |
2102 |
|
2789 |
|
|
* samples/water/tip3p_ice/tp3.md: fixed a sample |
2790 |
|
|
|
2791 |
gezelter |
2199 |
2004-12-01 14:10 tim |
2792 |
tim |
2102 |
|
2793 |
|
|
* src/math/RectMatrix.hpp, src/primitives/DirectionalAtom.cpp, |
2794 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
2795 |
|
|
src/types/AtomType.hpp, src/utils/Utility.hpp, |
2796 |
|
|
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
2797 |
|
|
src/visitors/AtomVisitor.hpp, test/math/RectMatrixTestCase.cpp: |
2798 |
|
|
spell check |
2799 |
|
|
|
2800 |
gezelter |
2199 |
2004-12-01 13:42 tim |
2801 |
tim |
2102 |
|
2802 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
2803 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
2804 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, primitives/Atom.hpp, |
2805 |
|
|
primitives/DirectionalAtom.cpp, primitives/RigidBody.cpp, |
2806 |
|
|
primitives/StuntDouble.hpp, types/AtomType.cpp: except integrator |
2807 |
|
|
and constraint, other directories get built |
2808 |
|
|
|
2809 |
gezelter |
2199 |
2004-12-01 12:38 tim |
2810 |
tim |
2102 |
|
2811 |
|
|
* src/: brains/DataStorage.cpp, brains/DataStorage.hpp, |
2812 |
|
|
brains/ForceManager.cpp, brains/MoleculeCreator.cpp, |
2813 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
2814 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, |
2815 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
2816 |
|
|
primitives/GhostBend.cpp, primitives/RigidBody.cpp, |
2817 |
|
|
primitives/RigidBody.hpp, primitives/StuntDouble.hpp, |
2818 |
|
|
types/AtomType.cpp, types/AtomType.hpp, types/AtomTypeProperties.h, |
2819 |
|
|
types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp: |
2820 |
|
|
refactory AtomType |
2821 |
|
|
|
2822 |
gezelter |
2199 |
2004-11-30 22:11 tim |
2823 |
tim |
2102 |
|
2824 |
|
|
* src/: math/Vector.hpp, primitives/RigidBody.cpp: minor change |
2825 |
|
|
|
2826 |
gezelter |
2199 |
2004-11-30 21:30 tim |
2827 |
tim |
2102 |
|
2828 |
|
|
* src/utils/: NumericConstant.cpp, NumericConstant.hpp: Change |
2829 |
|
|
NumericConstant |
2830 |
|
|
|
2831 |
gezelter |
2199 |
2004-11-30 21:24 tim |
2832 |
tim |
2102 |
|
2833 |
|
|
* src/: UseTheForce/ForceField.cpp, io/SectionParser.cpp, |
2834 |
|
|
primitives/RigidBody.cpp: minor fix |
2835 |
|
|
|
2836 |
gezelter |
2199 |
2004-11-30 18:14 tim |
2837 |
tim |
2102 |
|
2838 |
|
|
* src/: brains/Stats.hpp, io/DumpReader.cpp, io/DumpReader.hpp, |
2839 |
|
|
io/DumpWrite.hpp, io/DumpWriter.cpp, io/Makefile, |
2840 |
|
|
io/StatWriter.cpp, io/StatWriter.hpp, utils/StringTokenizer.hpp: io |
2841 |
|
|
get built, next is integrator |
2842 |
|
|
|
2843 |
gezelter |
2199 |
2004-11-30 17:43 tim |
2844 |
tim |
2102 |
|
2845 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
2846 |
|
|
UseTheForce/ForceField.hpp, brains/SimCreator.cpp, |
2847 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
2848 |
|
|
io/BASS_interface.cpp, primitives/StuntDouble.hpp, |
2849 |
|
|
utils/StringUtils.hpp: brains get built |
2850 |
|
|
|
2851 |
gezelter |
2199 |
2004-11-30 15:50 tim |
2852 |
tim |
2102 |
|
2853 |
|
|
* src/: brains/ForceManager.cpp, brains/Makefile, |
2854 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
2855 |
|
|
primitives/RigidBody.cpp, primitives/RigidBody.hpp, |
2856 |
|
|
utils/StringUtils.hpp: brains get built, io is next |
2857 |
|
|
|
2858 |
gezelter |
2199 |
2004-11-30 14:58 tim |
2859 |
tim |
2102 |
|
2860 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
2861 |
|
|
brains/ForceManager.cpp, brains/ForceManager.hpp, |
2862 |
|
|
brains/MoleculeCreator.cpp, brains/SimCreator.hpp, |
2863 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, |
2864 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
2865 |
|
|
brains/SnapShot.cpp, brains/Stats.cpp, brains/Stats.hpp, |
2866 |
|
|
brains/Thermo.cpp, brains/Thermo.hpp, io/Makefile, |
2867 |
|
|
math/SquareMatrix3.hpp, utils/OOPSEConstant.hpp: fix Thermo |
2868 |
|
|
|
2869 |
gezelter |
2199 |
2004-11-30 14:58 tim |
2870 |
tim |
2102 |
|
2871 |
tim |
2116 |
* src/utils/OOPSEConstant.hpp: file OOPSEConstant.hpp was initially |
2872 |
|
|
added on branch new_design. |
2873 |
|
|
|
2874 |
gezelter |
2199 |
2004-11-30 12:54 tim |
2875 |
tim |
2116 |
|
2876 |
tim |
2102 |
* src/: primitives/Bend.hpp, primitives/Bond.hpp, |
2877 |
|
|
primitives/StuntDouble.hpp, primitives/Torsion.hpp, |
2878 |
|
|
utils/LocalIndexManager.hpp: more get fixed |
2879 |
|
|
|
2880 |
gezelter |
2199 |
2004-11-30 00:03 tim |
2881 |
tim |
2102 |
|
2882 |
tim |
2116 |
* src/utils/LocalIndexManager.hpp: file LocalIndexManager.hpp was |
2883 |
|
|
initially added on branch new_design. |
2884 |
|
|
|
2885 |
gezelter |
2199 |
2004-11-30 00:03 tim |
2886 |
tim |
2116 |
|
2887 |
tim |
2102 |
* src/utils/: LocalIndexManager.hpp, LocalndexManager.hpp: rename |
2888 |
|
|
LocalndexManager.hpp to LocalIndexManager.hpp |
2889 |
|
|
|
2890 |
gezelter |
2199 |
2004-11-29 23:43 tim |
2891 |
tim |
2102 |
|
2892 |
|
|
* src/: io/BendTypesSectionParser.cpp, |
2893 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
2894 |
|
|
io/BondTypesSectionParser.hpp, io/SectionParserManager.cpp, |
2895 |
|
|
io/SectionParserManager.hpp, io/TorsionTypesSectionParser.cpp, |
2896 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
2897 |
|
|
types/PolynomialTorsionType.hpp: Section Parsers get compiled |
2898 |
|
|
|
2899 |
gezelter |
2199 |
2004-11-29 23:14 tim |
2900 |
tim |
2102 |
|
2901 |
|
|
* src/: io/BendTypesSectionParser.cpp, |
2902 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
2903 |
|
|
io/BondTypesSectionParser.hpp, io/TorsionTypesSectionParser.cpp, |
2904 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp: minor |
2905 |
|
|
fixed |
2906 |
|
|
|
2907 |
gezelter |
2199 |
2004-11-29 22:49 tim |
2908 |
tim |
2102 |
|
2909 |
|
|
* src/: io/TorsionTypesSectionParser.cpp, |
2910 |
|
|
io/TorsionTypesSectionParser.hpp, types/CharmmTorsionType.hpp, |
2911 |
|
|
types/CubicTorsionType.hpp, types/PolynomialBendType.hpp, |
2912 |
|
|
types/PolynomialBondType.hpp, types/PolynomialTorsionType.hpp, |
2913 |
|
|
types/QuarticTorsionType.hpp: minor fixed |
2914 |
|
|
|
2915 |
gezelter |
2199 |
2004-11-29 22:32 tim |
2916 |
tim |
2102 |
|
2917 |
|
|
* src/: io/TorsionTypesSectionParser.cpp, |
2918 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
2919 |
|
|
types/PolynomialTorsionType.hpp: #inlcude statement can not be |
2920 |
|
|
embedded |
2921 |
|
|
|
2922 |
gezelter |
2199 |
2004-11-29 16:42 tim |
2923 |
tim |
2102 |
|
2924 |
|
|
* test/math/: Makefile, PolynomialTestCase.cpp, |
2925 |
|
|
PolynomialTestCase.hpp: add PolynomialTestCase |
2926 |
|
|
|
2927 |
gezelter |
2199 |
2004-11-29 16:42 tim |
2928 |
tim |
2102 |
|
2929 |
|
|
* src/math/Polynomial.hpp: Polynomial passes unit test |
2930 |
|
|
|
2931 |
gezelter |
2199 |
2004-11-29 15:03 tim |
2932 |
tim |
2102 |
|
2933 |
|
|
* src/types/: QuarticTorsion.hpp, QuarticTorsionType.hpp: rename |
2934 |
|
|
QuarticTorsion.hpp to QuarticTorsionType.hpp |
2935 |
|
|
|
2936 |
gezelter |
2199 |
2004-11-29 15:03 tim |
2937 |
tim |
2102 |
|
2938 |
|
|
* src/types/QuarticTorsionType.hpp: file QuarticTorsionType.hpp was |
2939 |
|
|
initially added on branch new_design. |
2940 |
|
|
|
2941 |
gezelter |
2199 |
2004-11-29 14:56 tim |
2942 |
tim |
2102 |
|
2943 |
|
|
* src/types/CubicTorsionType.hpp: file CubicTorsionType.hpp was |
2944 |
|
|
initially added on branch new_design. |
2945 |
|
|
|
2946 |
gezelter |
2199 |
2004-11-29 14:56 tim |
2947 |
tim |
2102 |
|
2948 |
|
|
* src/types/: CubicTorsionType.hpp, QuarticTorsion.hpp: add |
2949 |
|
|
CubicTorsionType and QuarticTorsionType |
2950 |
|
|
|
2951 |
gezelter |
2199 |
2004-11-29 14:56 tim |
2952 |
tim |
2102 |
|
2953 |
|
|
* src/types/QuarticTorsion.hpp: file QuarticTorsion.hpp was |
2954 |
|
|
initially added on branch new_design. |
2955 |
|
|
|
2956 |
gezelter |
2199 |
2004-11-29 13:00 tim |
2957 |
tim |
2102 |
|
2958 |
|
|
* src/: brains/DataStorage.hpp, brains/Snapshot.hpp, |
2959 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
2960 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp: more file get |
2961 |
|
|
fixed |
2962 |
|
|
|
2963 |
gezelter |
2199 |
2004-11-29 12:59 tim |
2964 |
tim |
2102 |
|
2965 |
|
|
* src/utils/Trim.hpp: file Trim.hpp was initially added on branch |
2966 |
|
|
new_design. |
2967 |
|
|
|
2968 |
gezelter |
2199 |
2004-11-29 12:59 tim |
2969 |
tim |
2102 |
|
2970 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp, Trim.hpp: add Trim |
2971 |
|
|
Algorithm for std::string |
2972 |
|
|
|
2973 |
gezelter |
2199 |
2004-11-29 10:52 tim |
2974 |
tim |
2102 |
|
2975 |
|
|
* src/UseTheForce/: EAM.cpp, EAM.hpp, LJFF.cpp, LJFF.hpp: remove |
2976 |
|
|
some useless files |
2977 |
|
|
|
2978 |
gezelter |
2199 |
2004-11-29 10:50 tim |
2979 |
tim |
2102 |
|
2980 |
|
|
* src/io/: BondTypesSectionParser.cpp, |
2981 |
|
|
ChargeAtomTypesSectionParser.cpp, DipoleAtomTypesSectionParser.cpp, |
2982 |
|
|
ElectrostaticAtomTypesSectionParser.cpp, |
2983 |
|
|
HarmonicBondTypesSectionParser.cpp, |
2984 |
|
|
HarmonicBondTypesSectionParser.hpp, |
2985 |
|
|
LennardJonesAtomTypesSectionParser.cpp, Makefile, |
2986 |
|
|
SectionParserManager.cpp, StickyAtomTypesSectionParser.cpp, |
2987 |
|
|
StickyAtomTypesSectionParser.hpp: more files get fixed |
2988 |
|
|
|
2989 |
gezelter |
2199 |
2004-11-29 10:27 tim |
2990 |
tim |
2102 |
|
2991 |
|
|
* src/io/: AtomTypesSectionParser.cpp, BendTypesSectionParser.cpp, |
2992 |
|
|
DirectionalAtomTypesSectionParser.cpp, |
2993 |
|
|
EAMAtomTypesSectionParser.cpp, EAMAtomTypesSectionParser.hpp, |
2994 |
|
|
Makefile, SectionParser.cpp, SectionParser.hpp, |
2995 |
|
|
SectionParserManager.cpp, SectionParserManager.hpp: part of io get |
2996 |
|
|
built |
2997 |
|
|
|
2998 |
gezelter |
2199 |
2004-11-29 09:49 tim |
2999 |
tim |
2102 |
|
3000 |
|
|
* src/types/UreyBradleyBendType.hpp: types get built |
3001 |
|
|
|
3002 |
gezelter |
2199 |
2004-11-29 09:40 tim |
3003 |
tim |
2102 |
|
3004 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.cpp: |
3005 |
|
|
types get built |
3006 |
|
|
|
3007 |
gezelter |
2199 |
2004-11-25 21:13 tim |
3008 |
tim |
2102 |
|
3009 |
|
|
* src/: UseTheForce/ForceField.hpp, |
3010 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, math/Polynomial.hpp, |
3011 |
|
|
types/CubicBendType.hpp, types/PolynomialBendType.hpp: rename some |
3012 |
|
|
files |
3013 |
|
|
|
3014 |
gezelter |
2199 |
2004-11-25 15:18 tim |
3015 |
tim |
2102 |
|
3016 |
tim |
2116 |
* src/types/QuarticBondType.hpp: file QuarticBondType.hpp was |
3017 |
|
|
initially added on branch new_design. |
3018 |
|
|
|
3019 |
gezelter |
2199 |
2004-11-25 15:18 tim |
3020 |
tim |
2116 |
|
3021 |
tim |
2102 |
* src/: io/AtomTypesSectionParser.cpp, |
3022 |
|
|
io/BondTypesSectionParser.cpp, |
3023 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
3024 |
|
|
types/QuadraticBendType.hpp, types/QuadraticBondType.hpp, |
3025 |
|
|
types/QuarticBendType.hpp, types/QuarticBondType.hpp: rename some |
3026 |
|
|
files |
3027 |
|
|
|
3028 |
gezelter |
2199 |
2004-11-25 15:18 tim |
3029 |
tim |
2102 |
|
3030 |
|
|
* src/types/QuarticBendType.hpp: file QuarticBendType.hpp was |
3031 |
|
|
initially added on branch new_design. |
3032 |
|
|
|
3033 |
gezelter |
2199 |
2004-11-24 17:12 tim |
3034 |
tim |
2102 |
|
3035 |
|
|
* src/: io/AtomTypesSectionParser.cpp, |
3036 |
|
|
io/AtomTypesSectionParser.hpp, io/BendTypesSectionParser.cpp, |
3037 |
|
|
io/BendTypesSectionParser.hpp, io/BondTypesSectionParser.cpp, |
3038 |
|
|
io/BondTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
3039 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
3040 |
|
|
io/DipoleAtomTypesSectionParser.cpp, |
3041 |
|
|
io/DipoleAtomTypesSectionParser.hpp, |
3042 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, io/DumpReader.cpp, |
3043 |
|
|
io/DumpReader.hpp, io/EAMAtomTypesSectionParser.cpp, |
3044 |
|
|
io/EAMAtomTypesSectionParser.hpp, |
3045 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
3046 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, |
3047 |
|
|
io/HarmonicBondTypesSectionParser.hpp, |
3048 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, |
3049 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/Makefile, |
3050 |
|
|
io/SectionParser.hpp, io/SectionParserManager.hpp, |
3051 |
|
|
io/StickyAtomTypesSectionParser.cpp, |
3052 |
|
|
io/StickyAtomTypesSectionParser.hpp, |
3053 |
|
|
io/TorsionTypesSectionParser.cpp, io/TorsionTypesSectionParser.hpp, |
3054 |
|
|
utils/LocalndexManager.hpp, utils/TypeContainer.hpp: more get built |
3055 |
|
|
|
3056 |
gezelter |
2199 |
2004-11-24 16:33 tim |
3057 |
tim |
2102 |
|
3058 |
|
|
* src/UseTheForce/: DUFF.cpp, DUFF.hpp, EAM.cpp, ForceField.cpp, |
3059 |
|
|
ForceField.hpp, ForceFieldFactory.cpp, ForceFieldFactory.hpp, |
3060 |
|
|
LJFF.cpp, Makefile: UseTheForce get built |
3061 |
|
|
|
3062 |
gezelter |
2199 |
2004-11-24 15:55 tim |
3063 |
tim |
2102 |
|
3064 |
|
|
* src/: math/RectMatrix.hpp, primitives/Bend.cpp, |
3065 |
|
|
primitives/Bend.hpp, primitives/Bond.hpp, primitives/GhostBend.cpp, |
3066 |
|
|
primitives/Makefile, primitives/Molecule.cpp, |
3067 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
3068 |
|
|
primitives/StuntDouble.hpp, primitives/Torsion.cpp, |
3069 |
|
|
primitives/Torsion.hpp, primitives/UreyBradleyBend.cpp, |
3070 |
|
|
primitives/UreyBradleyBend.hpp: types and primitives get built |
3071 |
|
|
|
3072 |
gezelter |
2199 |
2004-11-24 14:49 tim |
3073 |
tim |
2102 |
|
3074 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
3075 |
|
|
StringTokenizerTestCase.cpp, StringTokenizerTestCase.hpp: Addint |
3076 |
|
|
StringTokenizerTestCase |
3077 |
|
|
|
3078 |
gezelter |
2199 |
2004-11-24 14:49 tim |
3079 |
tim |
2102 |
|
3080 |
|
|
* src/utils/: GenericData.hpp, StringTokenizer.cpp, |
3081 |
|
|
StringTokenizer.hpp: StringTokenizer passes unit test |
3082 |
|
|
|
3083 |
gezelter |
2199 |
2004-11-24 13:20 tim |
3084 |
tim |
2102 |
|
3085 |
|
|
* ChangeLog, make/Makefile.in, src/UseTheForce/Makefile, |
3086 |
|
|
src/io/Makefile, src/primitives/Makefile, src/utils/Makefile: |
3087 |
|
|
change Makefile |
3088 |
|
|
|
3089 |
gezelter |
2199 |
2004-11-24 13:06 chrisfen |
3090 |
tim |
2102 |
|
3091 |
|
|
* src/io/RestraintReader.cpp: improved restraints - mpi should work |
3092 |
|
|
fine |
3093 |
|
|
|
3094 |
gezelter |
2199 |
2004-11-24 13:06 chrisfen |
3095 |
tim |
2102 |
|
3096 |
|
|
* src/integrators/Integrator.cpp: improved restraints |
3097 |
|
|
|
3098 |
gezelter |
2199 |
2004-11-24 13:05 chrisfen |
3099 |
tim |
2102 |
|
3100 |
|
|
* samples/water/tip3p_ice/tp3.md: oops... |
3101 |
|
|
|
3102 |
gezelter |
2199 |
2004-11-24 12:42 tim |
3103 |
tim |
1779 |
|
3104 |
|
|
* src/: applications/oopse/oopse.cpp, brains/DataStorage.cpp, |
3105 |
|
|
brains/DataStorage.hpp, brains/SimCreator.cpp, |
3106 |
|
|
brains/SimCreator.hpp, integrators/Integrator.hpp, |
3107 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
3108 |
|
|
primitives/DirectionalAtom.cpp: add SetForceManager method to |
3109 |
|
|
integrator |
3110 |
|
|
|
3111 |
gezelter |
2199 |
2004-11-23 18:12 tim |
3112 |
tim |
1779 |
|
3113 |
|
|
* src/: brains/MoleculeCreator.cpp, integrators/Integrator.hpp, |
3114 |
|
|
integrators/NPT.cpp, integrators/NPT.hpp, integrators/NPTf.cpp, |
3115 |
|
|
integrators/NPTf.hpp, integrators/NPTi.cpp, integrators/NPTi.hpp, |
3116 |
|
|
integrators/NPTxyz.cpp, integrators/NPTxyz.hpp, |
3117 |
|
|
integrators/NVE.cpp, integrators/NVE.hpp, integrators/NVT.cpp, |
3118 |
|
|
integrators/NVT.hpp, integrators/Velocitizer.cpp, |
3119 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
3120 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
3121 |
|
|
types/UreyBradleyBendType.hpp: refactory NPT integrator |
3122 |
|
|
|
3123 |
gezelter |
2199 |
2004-11-23 17:50 chrisfen |
3124 |
tim |
1779 |
|
3125 |
|
|
* samples/water/tip3p_ice/tp3.md: Back to normal... Oh... |
3126 |
|
|
Restraints should work in parallel now |
3127 |
|
|
|
3128 |
gezelter |
2199 |
2004-11-23 17:48 chrisfen |
3129 |
tim |
1779 |
|
3130 |
|
|
* src/: UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
3131 |
|
|
brains/ForceFields.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
3132 |
|
|
integrators/Integrator.cpp, integrators/Integrator.hpp, |
3133 |
|
|
io/DumpWriter.cpp, io/Makefile, io/ReadWrite.hpp, |
3134 |
|
|
io/RestraintReader.cpp, io/RestraintWriter.cpp, |
3135 |
|
|
restraints/Restraints.cpp, restraints/Restraints.hpp: Improvements |
3136 |
|
|
to restraints |
3137 |
|
|
|
3138 |
gezelter |
2199 |
2004-11-23 17:47 chrisfen |
3139 |
tim |
1779 |
|
3140 |
|
|
* samples/water/tip3p_ice/tp3.md: just some testing changes, I'll |
3141 |
|
|
return to the original on next commit |
3142 |
|
|
|
3143 |
gezelter |
2199 |
2004-11-23 12:53 tim |
3144 |
tim |
1779 |
|
3145 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3146 |
|
|
UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
3147 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
3148 |
|
|
io/ChargeAtomTypesSectionParser.cpp, |
3149 |
|
|
io/DirectionalAtomTypesSectionParser.hpp, |
3150 |
|
|
io/EAMAtomTypesSectionParser.cpp, |
3151 |
|
|
io/ElectrostaticAtomTypesSectionParser.cpp, |
3152 |
|
|
io/ElectrostaticAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
3153 |
|
|
io/SectionParser.hpp, types/DirectionalAtomType.cpp, |
3154 |
|
|
utils/TypeContainer.hpp: add Electrostatic AtomType Section Parser |
3155 |
|
|
|
3156 |
gezelter |
2199 |
2004-11-23 12:53 tim |
3157 |
tim |
1779 |
|
3158 |
|
|
* src/io/ElectrostaticAtomTypesSectionParser.hpp: file |
3159 |
|
|
ElectrostaticAtomTypesSectionParser.hpp was initially added on |
3160 |
|
|
branch new_design. |
3161 |
|
|
|
3162 |
gezelter |
2199 |
2004-11-23 12:53 tim |
3163 |
tim |
1779 |
|
3164 |
tim |
2116 |
* src/io/ElectrostaticAtomTypesSectionParser.cpp: file |
3165 |
|
|
ElectrostaticAtomTypesSectionParser.cpp was initially added on |
3166 |
|
|
branch new_design. |
3167 |
tim |
1779 |
|
3168 |
gezelter |
2199 |
2004-11-23 01:03 tim |
3169 |
tim |
1779 |
|
3170 |
|
|
* src/: io/EAMAtomTypesSectionParser.cpp, |
3171 |
|
|
io/EAMAtomTypesSectionParser.hpp, types/AtomType.cpp, |
3172 |
|
|
types/AtomType.hpp, types/DirectionalAtomType.cpp, |
3173 |
|
|
types/DirectionalAtomType.hpp: add EAM AtomType Section Parser |
3174 |
|
|
|
3175 |
gezelter |
2199 |
2004-11-23 01:03 tim |
3176 |
tim |
1779 |
|
3177 |
tim |
2116 |
* src/types/DirectionalAtomType.cpp: file DirectionalAtomType.cpp |
3178 |
|
|
was initially added on branch new_design. |
3179 |
|
|
|
3180 |
gezelter |
2199 |
2004-11-23 01:03 tim |
3181 |
tim |
2116 |
|
3182 |
tim |
1779 |
* src/io/EAMAtomTypesSectionParser.hpp: file |
3183 |
|
|
EAMAtomTypesSectionParser.hpp was initially added on branch |
3184 |
|
|
new_design. |
3185 |
|
|
|
3186 |
gezelter |
2199 |
2004-11-23 01:03 tim |
3187 |
tim |
1779 |
|
3188 |
tim |
2116 |
* src/io/EAMAtomTypesSectionParser.cpp: file |
3189 |
|
|
EAMAtomTypesSectionParser.cpp was initially added on branch |
3190 |
|
|
new_design. |
3191 |
tim |
1779 |
|
3192 |
gezelter |
2199 |
2004-11-22 23:35 tim |
3193 |
tim |
1779 |
|
3194 |
tim |
2116 |
* src/io/TorsionTypesSectionParser.hpp: file |
3195 |
|
|
TorsionTypesSectionParser.hpp was initially added on branch |
3196 |
tim |
1779 |
new_design. |
3197 |
|
|
|
3198 |
gezelter |
2199 |
2004-11-22 23:35 tim |
3199 |
tim |
1779 |
|
3200 |
|
|
* src/io/BendTypesSectionParser.hpp: file |
3201 |
|
|
BendTypesSectionParser.hpp was initially added on branch |
3202 |
|
|
new_design. |
3203 |
|
|
|
3204 |
gezelter |
2199 |
2004-11-22 23:35 tim |
3205 |
tim |
1779 |
|
3206 |
|
|
* src/io/BondTypesSectionParser.hpp: file |
3207 |
|
|
BondTypesSectionParser.hpp was initially added on branch |
3208 |
|
|
new_design. |
3209 |
|
|
|
3210 |
gezelter |
2199 |
2004-11-22 23:35 tim |
3211 |
tim |
1779 |
|
3212 |
tim |
2116 |
* src/io/BondTypesSectionParser.cpp: file |
3213 |
|
|
BondTypesSectionParser.cpp was initially added on branch |
3214 |
tim |
1779 |
new_design. |
3215 |
|
|
|
3216 |
gezelter |
2199 |
2004-11-22 23:35 tim |
3217 |
tim |
1779 |
|
3218 |
tim |
2116 |
* src/io/TorsionTypesSectionParser.cpp: file |
3219 |
|
|
TorsionTypesSectionParser.cpp was initially added on branch |
3220 |
tim |
1779 |
new_design. |
3221 |
|
|
|
3222 |
gezelter |
2199 |
2004-11-22 23:35 tim |
3223 |
tim |
1779 |
|
3224 |
|
|
* src/io/: BendTypesSectionParser.cpp, BendTypesSectionParser.hpp, |
3225 |
|
|
BondTypesSectionParser.cpp, BondTypesSectionParser.hpp, |
3226 |
|
|
TorsionTypesSectionParser.cpp, TorsionTypesSectionParser.hpp: add |
3227 |
|
|
BondTypesSectionParser, BendTypesSectionParser and |
3228 |
|
|
TorsionTypeSectionParser |
3229 |
|
|
|
3230 |
gezelter |
2199 |
2004-11-22 23:35 tim |
3231 |
tim |
1779 |
|
3232 |
tim |
2116 |
* src/io/BendTypesSectionParser.cpp: file |
3233 |
|
|
BendTypesSectionParser.cpp was initially added on branch |
3234 |
|
|
new_design. |
3235 |
|
|
|
3236 |
gezelter |
2199 |
2004-11-22 18:04 tim |
3237 |
tim |
2116 |
|
3238 |
tim |
1779 |
* src/UseTheForce/: DUFF.cpp, EAM.cpp, EAM.hpp: minor change in |
3239 |
|
|
DUFF and EAM |
3240 |
|
|
|
3241 |
gezelter |
2199 |
2004-11-22 18:02 tim |
3242 |
tim |
1779 |
|
3243 |
tim |
2116 |
* src/io/: DirectionalAtomTypesParser.hpp, |
3244 |
|
|
DirectionalAtomTypesSectionParser.hpp: adding section parsers |
3245 |
|
|
|
3246 |
gezelter |
2199 |
2004-11-22 18:02 tim |
3247 |
tim |
2116 |
|
3248 |
tim |
1779 |
* src/io/DirectionalAtomTypesSectionParser.hpp: file |
3249 |
|
|
DirectionalAtomTypesSectionParser.hpp was initially added on branch |
3250 |
|
|
new_design. |
3251 |
|
|
|
3252 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3253 |
tim |
1779 |
|
3254 |
tim |
2116 |
* src/io/DipoleAtomTypesSectionParser.hpp: file |
3255 |
|
|
DipoleAtomTypesSectionParser.hpp was initially added on branch |
3256 |
|
|
new_design. |
3257 |
tim |
1779 |
|
3258 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3259 |
tim |
1779 |
|
3260 |
tim |
2116 |
* src/io/AtomTypesSectionParser.hpp: file |
3261 |
|
|
AtomTypesSectionParser.hpp was initially added on branch |
3262 |
tim |
1779 |
new_design. |
3263 |
|
|
|
3264 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3265 |
tim |
1779 |
|
3266 |
|
|
* src/io/HarmonicBondTypesSectionParser.hpp: file |
3267 |
|
|
HarmonicBondTypesSectionParser.hpp was initially added on branch |
3268 |
|
|
new_design. |
3269 |
|
|
|
3270 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3271 |
tim |
1779 |
|
3272 |
tim |
2116 |
* src/io/StickyAtomTypesSectionParser.cpp: file |
3273 |
|
|
StickyAtomTypesSectionParser.cpp was initially added on branch |
3274 |
tim |
1779 |
new_design. |
3275 |
|
|
|
3276 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3277 |
tim |
1779 |
|
3278 |
tim |
2116 |
* src/io/LennardJonesAtomTypesSectionParser.hpp: file |
3279 |
|
|
LennardJonesAtomTypesSectionParser.hpp was initially added on |
3280 |
|
|
branch new_design. |
3281 |
|
|
|
3282 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3283 |
tim |
2116 |
|
3284 |
|
|
* src/io/HarmonicBondTypesSectionParser.cpp: file |
3285 |
|
|
HarmonicBondTypesSectionParser.cpp was initially added on branch |
3286 |
|
|
new_design. |
3287 |
|
|
|
3288 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3289 |
tim |
2116 |
|
3290 |
tim |
2102 |
* src/io/DirectionalAtomTypesSectionParser.cpp: file |
3291 |
|
|
DirectionalAtomTypesSectionParser.cpp was initially added on branch |
3292 |
|
|
new_design. |
3293 |
|
|
|
3294 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3295 |
tim |
2102 |
|
3296 |
tim |
2116 |
* src/io/SectionParserManager.cpp: file SectionParserManager.cpp |
3297 |
|
|
was initially added on branch new_design. |
3298 |
|
|
|
3299 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3300 |
tim |
2116 |
|
3301 |
|
|
* src/io/AtomTypesSectionParser.cpp: file |
3302 |
|
|
AtomTypesSectionParser.cpp was initially added on branch |
3303 |
|
|
new_design. |
3304 |
|
|
|
3305 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3306 |
tim |
2116 |
|
3307 |
|
|
* src/io/ChargeAtomTypesSectionParser.cpp: file |
3308 |
|
|
ChargeAtomTypesSectionParser.cpp was initially added on branch |
3309 |
|
|
new_design. |
3310 |
|
|
|
3311 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3312 |
tim |
2116 |
|
3313 |
|
|
* src/io/DipoleAtomTypesSectionParser.cpp: file |
3314 |
|
|
DipoleAtomTypesSectionParser.cpp was initially added on branch |
3315 |
|
|
new_design. |
3316 |
|
|
|
3317 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3318 |
tim |
2116 |
|
3319 |
tim |
2102 |
* src/io/LennardJonesAtomTypesSectionParser.cpp: file |
3320 |
|
|
LennardJonesAtomTypesSectionParser.cpp was initially added on |
3321 |
tim |
1779 |
branch new_design. |
3322 |
|
|
|
3323 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3324 |
tim |
1779 |
|
3325 |
tim |
2116 |
* src/io/ChargeAtomTypesSectionParser.hpp: file |
3326 |
|
|
ChargeAtomTypesSectionParser.hpp was initially added on branch |
3327 |
tim |
1779 |
new_design. |
3328 |
|
|
|
3329 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3330 |
tim |
1779 |
|
3331 |
tim |
2116 |
* src/io/StickyAtomTypesSectionParser.hpp: file |
3332 |
|
|
StickyAtomTypesSectionParser.hpp was initially added on branch |
3333 |
|
|
new_design. |
3334 |
|
|
|
3335 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3336 |
tim |
2116 |
|
3337 |
|
|
* src/io/SectionParser.hpp: file SectionParser.hpp was initially |
3338 |
|
|
added on branch new_design. |
3339 |
|
|
|
3340 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3341 |
tim |
2116 |
|
3342 |
tim |
2102 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/ForceField.hpp, |
3343 |
|
|
brains/SimSnapshotManager.cpp, brains/SnapShot.cpp, |
3344 |
|
|
brains/Snapshot.hpp, integrators/NVE.cpp, integrators/NVT.cpp, |
3345 |
|
|
integrators/NVT.hpp, io/AtomTypesSectionParser.cpp, |
3346 |
|
|
io/AtomTypesSectionParser.hpp, io/ChargeAtomTypesSectionParser.cpp, |
3347 |
|
|
io/ChargeAtomTypesSectionParser.hpp, |
3348 |
|
|
io/DipoleAtomTypesSectionParser.cpp, |
3349 |
|
|
io/DipoleAtomTypesSectionParser.hpp, |
3350 |
|
|
io/DirectionalAtomTypesParser.hpp, |
3351 |
|
|
io/DirectionalAtomTypesSectionParser.cpp, |
3352 |
|
|
io/HarmonicBondTypesSectionParser.cpp, |
3353 |
|
|
io/HarmonicBondTypesSectionParser.hpp, |
3354 |
|
|
io/LennardJonesAtomTypesSectionParser.cpp, |
3355 |
|
|
io/LennardJonesAtomTypesSectionParser.hpp, io/SectionParser.cpp, |
3356 |
|
|
io/SectionParser.hpp, io/SectionParserManager.cpp, |
3357 |
|
|
io/SectionParserManager.hpp, io/StickyAtomTypesSectionParser.cpp, |
3358 |
|
|
io/StickyAtomTypesSectionParser.hpp, primitives/StuntDouble.hpp, |
3359 |
|
|
types/AtomType.hpp, types/DirectionalAtomType.hpp, |
3360 |
|
|
utils/GenericData.hpp: adding section parsers |
3361 |
|
|
|
3362 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3363 |
tim |
2102 |
|
3364 |
tim |
2116 |
* src/io/DirectionalAtomTypesParser.hpp: file |
3365 |
|
|
DirectionalAtomTypesParser.hpp was initially added on branch |
3366 |
tim |
1779 |
new_design. |
3367 |
|
|
|
3368 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3369 |
tim |
1779 |
|
3370 |
tim |
2102 |
* src/io/SectionParserManager.hpp: file SectionParserManager.hpp |
3371 |
tim |
1779 |
was initially added on branch new_design. |
3372 |
|
|
|
3373 |
gezelter |
2199 |
2004-11-22 15:55 tim |
3374 |
tim |
1779 |
|
3375 |
tim |
2116 |
* src/io/SectionParser.cpp: file SectionParser.cpp was initially |
3376 |
|
|
added on branch new_design. |
3377 |
tim |
1779 |
|
3378 |
gezelter |
2199 |
2004-11-19 17:12 tim |
3379 |
tim |
1779 |
|
3380 |
tim |
2116 |
* src/types/FixedBondType.hpp: file FixedBondType.hpp was initially |
3381 |
tim |
1779 |
added on branch new_design. |
3382 |
|
|
|
3383 |
gezelter |
2199 |
2004-11-19 17:12 tim |
3384 |
tim |
1779 |
|
3385 |
|
|
* src/: brains/SimState.cpp, brains/SimState.hpp, |
3386 |
|
|
io/InitializeFromFile.cpp, types/FixBondType.hpp, |
3387 |
|
|
types/FixedBondType.hpp: remove more useless files |
3388 |
|
|
|
3389 |
gezelter |
2199 |
2004-11-19 16:47 tim |
3390 |
tim |
2102 |
|
3391 |
tim |
1779 |
* src/: UseTheForce/EAM_FF.cpp, UseTheForce/WATER.cpp, |
3392 |
|
|
integrators/Integrator.cpp, applications/Makedepend: remove more |
3393 |
|
|
useless files |
3394 |
|
|
|
3395 |
gezelter |
2199 |
2004-11-19 16:38 tim |
3396 |
tim |
1779 |
|
3397 |
tim |
2116 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3398 |
|
|
UseTheForce/EAM.cpp, integrators/NPT.hpp, integrators/NPTf.hpp, |
3399 |
|
|
integrators/NPTi.hpp, integrators/NPTxyz.hpp, integrators/NVT.cpp, |
3400 |
|
|
integrators/NVT.hpp: refactory integrator |
3401 |
|
|
|
3402 |
gezelter |
2199 |
2004-11-19 16:38 tim |
3403 |
tim |
2116 |
|
3404 |
tim |
1779 |
* src/integrators/NPTi.hpp: file NPTi.hpp was initially added on |
3405 |
|
|
branch new_design. |
3406 |
|
|
|
3407 |
gezelter |
2199 |
2004-11-19 16:38 tim |
3408 |
tim |
1779 |
|
3409 |
tim |
2116 |
* src/integrators/NPTf.hpp: file NPTf.hpp was initially added on |
3410 |
|
|
branch new_design. |
3411 |
tim |
1779 |
|
3412 |
gezelter |
2199 |
2004-11-19 16:38 tim |
3413 |
tim |
1779 |
|
3414 |
|
|
* src/integrators/NPT.hpp: file NPT.hpp was initially added on |
3415 |
|
|
branch new_design. |
3416 |
|
|
|
3417 |
gezelter |
2199 |
2004-11-19 16:38 tim |
3418 |
tim |
1779 |
|
3419 |
tim |
2116 |
* src/integrators/NPTxyz.hpp: file NPTxyz.hpp was initially added |
3420 |
|
|
on branch new_design. |
3421 |
tim |
1779 |
|
3422 |
gezelter |
2199 |
2004-11-19 16:38 tim |
3423 |
tim |
1779 |
|
3424 |
tim |
2116 |
* src/integrators/NVT.hpp: file NVT.hpp was initially added on |
3425 |
tim |
1779 |
branch new_design. |
3426 |
|
|
|
3427 |
gezelter |
2199 |
2004-11-19 15:37 tim |
3428 |
tim |
2102 |
|
3429 |
tim |
2116 |
* forceFields/newDUFF.frc: new DUFF forcefield |
3430 |
tim |
2102 |
|
3431 |
gezelter |
2199 |
2004-11-19 15:23 tim |
3432 |
tim |
1779 |
|
3433 |
tim |
2116 |
* src/UseTheForce/EAM.hpp: file EAM.hpp was initially added on |
3434 |
|
|
branch new_design. |
3435 |
tim |
1779 |
|
3436 |
gezelter |
2199 |
2004-11-19 15:23 tim |
3437 |
tim |
1779 |
|
3438 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM.cpp, |
3439 |
|
|
UseTheForce/EAM.hpp, UseTheForce/ForceField.hpp, |
3440 |
|
|
utils/TypeContainer.hpp: add EAM |
3441 |
|
|
|
3442 |
gezelter |
2199 |
2004-11-19 15:23 tim |
3443 |
tim |
1779 |
|
3444 |
|
|
* src/UseTheForce/EAM.cpp: file EAM.cpp was initially added on |
3445 |
|
|
branch new_design. |
3446 |
|
|
|
3447 |
gezelter |
2199 |
2004-11-19 13:02 tim |
3448 |
tim |
2102 |
|
3449 |
tim |
1779 |
* src/UseTheForce/: DUFF.cpp, DUFF.hpp: DUFF is almost done except |
3450 |
|
|
error checking |
3451 |
|
|
|
3452 |
gezelter |
2199 |
2004-11-19 12:56 tim |
3453 |
tim |
1779 |
|
3454 |
tim |
2116 |
* src/integrators/IntegratorFactory.hpp: file IntegratorFactory.hpp |
3455 |
tim |
1779 |
was initially added on branch new_design. |
3456 |
|
|
|
3457 |
gezelter |
2199 |
2004-11-19 12:56 tim |
3458 |
tim |
1779 |
|
3459 |
tim |
2116 |
* src/integrators/IntegratorFactory.cpp: file IntegratorFactory.cpp |
3460 |
tim |
1779 |
was initially added on branch new_design. |
3461 |
|
|
|
3462 |
gezelter |
2199 |
2004-11-19 12:56 tim |
3463 |
tim |
1779 |
|
3464 |
|
|
* src/types/FixBondType.hpp: file FixBondType.hpp was initially |
3465 |
|
|
added on branch new_design. |
3466 |
|
|
|
3467 |
gezelter |
2199 |
2004-11-19 12:56 tim |
3468 |
tim |
1779 |
|
3469 |
|
|
* src/: integrators/NVE.cpp, UseTheForce/DUFF.cpp, |
3470 |
|
|
UseTheForce/DUFF.hpp, UseTheForce/ForceField.cpp, |
3471 |
|
|
UseTheForce/ForceField.hpp, UseTheForce/ForceFieldFactory.cpp, |
3472 |
|
|
integrators/IntegratorFactory.cpp, |
3473 |
|
|
integrators/IntegratorFactory.hpp, integrators/NVE.hpp, |
3474 |
|
|
integrators/VelocityVerletIntegrator.hpp, types/FixBondType.hpp, |
3475 |
|
|
utils/StringTokenizer.cpp: DUFF is almost done except error |
3476 |
|
|
checking |
3477 |
|
|
|
3478 |
gezelter |
2199 |
2004-11-18 19:11 tim |
3479 |
tim |
1779 |
|
3480 |
|
|
* src/UseTheForce/DUFF.cpp: adding DUFF parser |
3481 |
|
|
|
3482 |
gezelter |
2199 |
2004-11-18 18:26 tim |
3483 |
tim |
1779 |
|
3484 |
tim |
2116 |
* src/integrators/Velocitizer.cpp: file Velocitizer.cpp was |
3485 |
|
|
initially added on branch new_design. |
3486 |
|
|
|
3487 |
gezelter |
2199 |
2004-11-18 18:26 tim |
3488 |
tim |
2116 |
|
3489 |
tim |
1779 |
* src/: UseTheForce/DUFF.hpp, integrators/NVE.cpp, |
3490 |
|
|
integrators/Velocitizer.cpp, integrators/Velocitizer.hpp, |
3491 |
|
|
integrators/VelocityVerletIntegrator.cpp, |
3492 |
|
|
integrators/VelocityVerletIntegrator.hpp, |
3493 |
|
|
types/CharmmTorsionType.cpp, types/CharmmTorsionType.hpp, |
3494 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
3495 |
|
|
types/HarmonicBondType.hpp, types/QuadraticBendType.hpp, |
3496 |
|
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: adding |
3497 |
|
|
DUFF parser |
3498 |
|
|
|
3499 |
gezelter |
2199 |
2004-11-18 16:42 tim |
3500 |
tim |
2102 |
|
3501 |
tim |
1779 |
* forceFields/newDUFF.frc: adding new format DUFF force field |
3502 |
|
|
|
3503 |
gezelter |
2199 |
2004-11-18 10:57 chrisfen |
3504 |
tim |
1779 |
|
3505 |
|
|
* src/UseTheForce/DarkSide/LJ.F90: Fixed a mixing list bug that |
3506 |
|
|
slowed down the force loop |
3507 |
|
|
|
3508 |
gezelter |
2199 |
2004-11-18 00:42 tim |
3509 |
tim |
1779 |
|
3510 |
tim |
2116 |
* src/utils/NumericConstant.cpp: file NumericConstant.cpp was |
3511 |
tim |
1779 |
initially added on branch new_design. |
3512 |
|
|
|
3513 |
gezelter |
2199 |
2004-11-18 00:42 tim |
3514 |
tim |
1779 |
|
3515 |
tim |
2116 |
* src/utils/NumericConstant.hpp: file NumericConstant.hpp was |
3516 |
tim |
1779 |
initially added on branch new_design. |
3517 |
|
|
|
3518 |
gezelter |
2199 |
2004-11-18 00:42 tim |
3519 |
tim |
1779 |
|
3520 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/LJFF.cpp, |
3521 |
|
|
primitives/Bend.cpp, utils/NumericConstant.cpp, |
3522 |
|
|
utils/NumericConstant.hpp: Adding NumericConstant class |
3523 |
|
|
|
3524 |
gezelter |
2199 |
2004-11-17 23:16 tim |
3525 |
tim |
1779 |
|
3526 |
|
|
* src/: applications/quickLate.c, UseTheForce/ForceFields.cpp, |
3527 |
|
|
UseTheForce/ForceFields.hpp: remove more junk files |
3528 |
|
|
|
3529 |
gezelter |
2199 |
2004-11-17 23:12 tim |
3530 |
tim |
1779 |
|
3531 |
|
|
* src/: brains/ForceFields.cpp, brains/SimSetup.cpp, |
3532 |
|
|
brains/SimSetup.hpp, constraints/AbstractClasses.hpp, |
3533 |
|
|
integrators/AbstractClasses.hpp, integrators/AllIntegrator.hpp, |
3534 |
|
|
primitives/AbstractClasses.hpp, primitives/Bond.cpp, |
3535 |
|
|
primitives/BondExtensions.cpp, primitives/SRI.hpp, |
3536 |
|
|
primitives/TorsionExtensions.cpp: remove some junk files |
3537 |
|
|
|
3538 |
gezelter |
2199 |
2004-11-17 23:07 tim |
3539 |
tim |
1779 |
|
3540 |
|
|
* src/primitives/BendExtensions.cpp: remove some junk files |
3541 |
|
|
|
3542 |
gezelter |
2199 |
2004-11-17 23:04 tim |
3543 |
tim |
1779 |
|
3544 |
|
|
* src/types/: PolynomialTorsionType.hpp, QuadraticBendType.hpp, |
3545 |
|
|
QuadraticBondType.hpp: refine QudraticBond |
3546 |
|
|
|
3547 |
gezelter |
2199 |
2004-11-17 22:57 tim |
3548 |
tim |
1779 |
|
3549 |
|
|
* src/types/QuadraticBendType.hpp: add QuadraticBendType.hpp |
3550 |
|
|
|
3551 |
gezelter |
2199 |
2004-11-17 22:57 tim |
3552 |
tim |
1779 |
|
3553 |
|
|
* src/types/QuadraticBendType.hpp: file QuadraticBendType.hpp was |
3554 |
|
|
initially added on branch new_design. |
3555 |
|
|
|
3556 |
gezelter |
2199 |
2004-11-17 16:47 tim |
3557 |
tim |
1779 |
|
3558 |
tim |
2116 |
* src/types/UreyBradleyBendType.hpp: file UreyBradleyBendType.hpp |
3559 |
|
|
was initially added on branch new_design. |
3560 |
|
|
|
3561 |
gezelter |
2199 |
2004-11-17 16:47 tim |
3562 |
tim |
2116 |
|
3563 |
tim |
1779 |
* src/types/CubicBendType.hpp: file CubicBendType.hpp was initially |
3564 |
|
|
added on branch new_design. |
3565 |
|
|
|
3566 |
gezelter |
2199 |
2004-11-17 16:47 tim |
3567 |
tim |
1779 |
|
3568 |
tim |
2116 |
* src/primitives/GhostBend.hpp: file GhostBend.hpp was initially |
3569 |
|
|
added on branch new_design. |
3570 |
|
|
|
3571 |
gezelter |
2199 |
2004-11-17 16:47 tim |
3572 |
tim |
2116 |
|
3573 |
tim |
1779 |
* src/types/QuadraticBondType.hpp: file QuadraticBondType.hpp was |
3574 |
|
|
initially added on branch new_design. |
3575 |
|
|
|
3576 |
gezelter |
2199 |
2004-11-17 16:47 tim |
3577 |
tim |
1779 |
|
3578 |
tim |
2116 |
* src/primitives/UreyBradleyBend.cpp: file UreyBradleyBend.cpp was |
3579 |
tim |
1779 |
initially added on branch new_design. |
3580 |
|
|
|
3581 |
gezelter |
2199 |
2004-11-17 16:47 tim |
3582 |
tim |
1779 |
|
3583 |
tim |
2116 |
* src/primitives/UreyBradleyBend.hpp: file UreyBradleyBend.hpp was |
3584 |
tim |
1779 |
initially added on branch new_design. |
3585 |
|
|
|
3586 |
gezelter |
2199 |
2004-11-17 16:47 tim |
3587 |
tim |
1779 |
|
3588 |
|
|
* src/types/CubicBondType.hpp: file CubicBondType.hpp was initially |
3589 |
|
|
added on branch new_design. |
3590 |
|
|
|
3591 |
gezelter |
2199 |
2004-11-17 16:47 tim |
3592 |
tim |
1779 |
|
3593 |
|
|
* src/: math/ChebyshevPolynomials.cpp, |
3594 |
|
|
math/ChebyshevPolynomials.hpp, primitives/Bend.cpp, |
3595 |
|
|
primitives/Bend.hpp, primitives/GhostBend.cpp, |
3596 |
|
|
primitives/GhostBend.hpp, primitives/UreyBradleyBend.cpp, |
3597 |
|
|
primitives/UreyBradleyBend.hpp, types/BondType.hpp, |
3598 |
|
|
types/CubicBendType.hpp, types/CubicBondType.hpp, |
3599 |
|
|
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
3600 |
|
|
types/QuadraticBondType.hpp, types/UreyBradleyBendType.hpp: |
3601 |
|
|
UreyBradleyBend and GhostBend |
3602 |
|
|
|
3603 |
gezelter |
2199 |
2004-11-17 13:58 tim |
3604 |
tim |
2102 |
|
3605 |
tim |
1779 |
* src/math/ChebyshevPolynomials.cpp: file ChebyshevPolynomials.cpp |
3606 |
|
|
was initially added on branch new_design. |
3607 |
|
|
|
3608 |
gezelter |
2199 |
2004-11-17 13:58 tim |
3609 |
tim |
1779 |
|
3610 |
|
|
* src/math/ChebyshevPolynomials.hpp: file ChebyshevPolynomials.hpp |
3611 |
|
|
was initially added on branch new_design. |
3612 |
|
|
|
3613 |
gezelter |
2199 |
2004-11-17 13:58 tim |
3614 |
tim |
1779 |
|
3615 |
|
|
* src/: math/ChebyshevPolynomials.cpp, |
3616 |
|
|
math/ChebyshevPolynomials.hpp, math/Polynomial.hpp, |
3617 |
|
|
primitives/Bond.hpp, types/CharmmTorsionType.hpp, |
3618 |
|
|
types/OplsTorsionType.hpp, types/PolynomialBondType.hpp, |
3619 |
|
|
types/PolynomialTorsionType.hpp, types/TorsionType.hpp: more types |
3620 |
|
|
stuff and Chebyshev Polynomial |
3621 |
|
|
|
3622 |
gezelter |
2199 |
2004-11-17 13:58 tim |
3623 |
tim |
1779 |
|
3624 |
tim |
2116 |
* src/types/OplsTorsionType.hpp: file OplsTorsionType.hpp was |
3625 |
tim |
1779 |
initially added on branch new_design. |
3626 |
|
|
|
3627 |
gezelter |
2199 |
2004-11-17 01:37 tim |
3628 |
tim |
1779 |
|
3629 |
tim |
2116 |
* src/types/PolynomialTorsionType.hpp: file |
3630 |
|
|
PolynomialTorsionType.hpp was initially added on branch new_design. |
3631 |
tim |
1779 |
|
3632 |
gezelter |
2199 |
2004-11-17 01:37 tim |
3633 |
tim |
1779 |
|
3634 |
|
|
* src/types/CharmmTorsionType.cpp: file CharmmTorsionType.cpp was |
3635 |
|
|
initially added on branch new_design. |
3636 |
|
|
|
3637 |
gezelter |
2199 |
2004-11-17 01:37 tim |
3638 |
tim |
1779 |
|
3639 |
|
|
* src/: math/Polynomial.hpp, primitives/Bend.cpp, |
3640 |
|
|
primitives/Bend.hpp, primitives/Torsion.cpp, types/BendType.hpp, |
3641 |
|
|
types/BondType.hpp, types/CharmmTorsionType.cpp, |
3642 |
|
|
types/CharmmTorsionType.hpp, types/HarmonicBendType.hpp, |
3643 |
|
|
types/HarmonicBondType.hpp, types/MorseBondType.hpp, |
3644 |
|
|
types/PolynomialBendType.hpp, types/PolynomialBondType.hpp, |
3645 |
|
|
types/PolynomialTorsionType.hpp, types/TorsionType.hpp, |
3646 |
|
|
utils/StringTokenizer.hpp: add PolynomialBondType, |
3647 |
|
|
PolynomialBendType, PolynomialTorsionType, HarmonicBendType and |
3648 |
|
|
CharmmTorsionType. Need to refine the design and add document for |
3649 |
|
|
them |
3650 |
|
|
|
3651 |
gezelter |
2199 |
2004-11-17 01:37 tim |
3652 |
tim |
1779 |
|
3653 |
tim |
2116 |
* src/types/CharmmTorsionType.hpp: file CharmmTorsionType.hpp was |
3654 |
|
|
initially added on branch new_design. |
3655 |
|
|
|
3656 |
gezelter |
2199 |
2004-11-17 01:37 tim |
3657 |
tim |
2116 |
|
3658 |
|
|
* src/types/HarmonicBendType.hpp: file HarmonicBendType.hpp was |
3659 |
|
|
initially added on branch new_design. |
3660 |
|
|
|
3661 |
gezelter |
2199 |
2004-11-17 01:37 tim |
3662 |
tim |
2116 |
|
3663 |
|
|
* src/types/PolynomialBendType.hpp: file PolynomialBendType.hpp was |
3664 |
|
|
initially added on branch new_design. |
3665 |
|
|
|
3666 |
gezelter |
2199 |
2004-11-16 20:11 tim |
3667 |
tim |
2116 |
|
3668 |
tim |
1779 |
* src/types/: BendType.hpp, PolynomialBondType.hpp, |
3669 |
|
|
TorsionType.hpp: add PolynomialBondType |
3670 |
|
|
|
3671 |
gezelter |
2199 |
2004-11-16 20:11 tim |
3672 |
tim |
1779 |
|
3673 |
|
|
* src/types/PolynomialBondType.hpp: file PolynomialBondType.hpp was |
3674 |
|
|
initially added on branch new_design. |
3675 |
|
|
|
3676 |
gezelter |
2199 |
2004-11-16 18:20 tim |
3677 |
tim |
1779 |
|
3678 |
|
|
* src/math/Polynomial.hpp: file Polynomial.hpp was initially added |
3679 |
|
|
on branch new_design. |
3680 |
|
|
|
3681 |
gezelter |
2199 |
2004-11-16 18:20 tim |
3682 |
tim |
1779 |
|
3683 |
tim |
2116 |
* src/math/Polynomial.hpp: Adding Polynomial class |
3684 |
tim |
1779 |
|
3685 |
gezelter |
2199 |
2004-11-16 17:04 gezelter |
3686 |
tim |
1779 |
|
3687 |
|
|
* src/types/MorseBondType.hpp: file MorseBondType.hpp was initially |
3688 |
|
|
added on branch new_design. |
3689 |
|
|
|
3690 |
gezelter |
2199 |
2004-11-16 17:04 gezelter |
3691 |
tim |
1779 |
|
3692 |
tim |
2116 |
* src/types/HarmonicBondType.hpp: file HarmonicBondType.hpp was |
3693 |
|
|
initially added on branch new_design. |
3694 |
|
|
|
3695 |
gezelter |
2199 |
2004-11-16 17:04 gezelter |
3696 |
tim |
2116 |
|
3697 |
tim |
1779 |
* src/types/: BendType.hpp, BondType.hpp, HarmonicBondType.hpp, |
3698 |
|
|
MorseBondType.hpp, TorsionType.hpp: added some new stuff |
3699 |
|
|
|
3700 |
gezelter |
2199 |
2004-11-16 15:36 tim |
3701 |
tim |
1779 |
|
3702 |
|
|
* src/: primitives/Bend.cpp, primitives/Bend.hpp, |
3703 |
|
|
primitives/Torsion.cpp, primitives/Torsion.hpp, types/BendType.hpp, |
3704 |
|
|
types/BondType.hpp, types/TorsionType.hpp: BondType, BendType and |
3705 |
|
|
TorsionType |
3706 |
|
|
|
3707 |
gezelter |
2199 |
2004-11-15 21:07 tim |
3708 |
tim |
1779 |
|
3709 |
tim |
2116 |
* src/UseTheForce/DUFF.hpp: file DUFF.hpp was initially added on |
3710 |
|
|
branch new_design. |
3711 |
|
|
|
3712 |
gezelter |
2199 |
2004-11-15 21:07 tim |
3713 |
tim |
2116 |
|
3714 |
tim |
1779 |
* src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp, |
3715 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/LJFF.hpp, |
3716 |
|
|
utils/StringTokenizer.cpp: adding DUFF class; adding checking |
3717 |
|
|
statement to nextTokenAsInt and nextTokenAsFloat in StringTokenizer |
3718 |
|
|
|
3719 |
gezelter |
2199 |
2004-11-15 18:00 tim |
3720 |
tim |
1779 |
|
3721 |
tim |
2116 |
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
3722 |
|
|
UseTheForce/ForceFieldFactory.cpp, |
3723 |
|
|
UseTheForce/ForceFieldFactory.hpp, UseTheForce/LJFF.cpp, |
3724 |
|
|
UseTheForce/LJFF.hpp, brains/SimCreator.cpp, types/AtomType.cpp, |
3725 |
|
|
types/AtomType.hpp: adding ForceFieldFactory and LJFF classes |
3726 |
tim |
1779 |
|
3727 |
gezelter |
2199 |
2004-11-15 18:00 tim |
3728 |
tim |
1779 |
|
3729 |
|
|
* src/UseTheForce/ForceFieldFactory.cpp: file ForceFieldFactory.cpp |
3730 |
|
|
was initially added on branch new_design. |
3731 |
|
|
|
3732 |
gezelter |
2199 |
2004-11-15 18:00 tim |
3733 |
tim |
1779 |
|
3734 |
tim |
2116 |
* src/UseTheForce/ForceFieldFactory.hpp: file ForceFieldFactory.hpp |
3735 |
|
|
was initially added on branch new_design. |
3736 |
|
|
|
3737 |
gezelter |
2199 |
2004-11-15 18:00 tim |
3738 |
tim |
2116 |
|
3739 |
tim |
2102 |
* src/UseTheForce/LJFF.hpp: file LJFF.hpp was initially added on |
3740 |
|
|
branch new_design. |
3741 |
tim |
1779 |
|
3742 |
gezelter |
2199 |
2004-11-15 13:02 tim |
3743 |
tim |
1779 |
|
3744 |
tim |
2116 |
* src/integrators/Velocitizer.hpp: file Velocitizer.hpp was |
3745 |
|
|
initially added on branch new_design. |
3746 |
tim |
1779 |
|
3747 |
gezelter |
2199 |
2004-11-15 13:02 tim |
3748 |
tim |
1779 |
|
3749 |
|
|
* src/io/DumpWrite.hpp: file DumpWrite.hpp was initially added on |
3750 |
|
|
branch new_design. |
3751 |
|
|
|
3752 |
gezelter |
2199 |
2004-11-15 13:02 tim |
3753 |
tim |
1779 |
|
3754 |
|
|
* src/io/DumpReader.hpp: file DumpReader.hpp was initially added on |
3755 |
|
|
branch new_design. |
3756 |
|
|
|
3757 |
gezelter |
2199 |
2004-11-15 13:02 tim |
3758 |
tim |
1779 |
|
3759 |
|
|
* src/: brains/SimInfo.cpp, brains/SimInfo.hpp, |
3760 |
|
|
brains/Snapshot.hpp, io/DumpReader.cpp, io/DumpWriter.cpp, |
3761 |
|
|
integrators/Velocitizer.hpp, io/DumpReader.hpp, io/DumpWrite.hpp, |
3762 |
|
|
io/ReadWrite.hpp, utils/StringTokenizer.hpp: finish DumpReader, |
3763 |
|
|
DumpWriter.Next Step is LJFF and integrators |
3764 |
|
|
|
3765 |
gezelter |
2199 |
2004-11-13 00:08 tim |
3766 |
tim |
1779 |
|
3767 |
|
|
* src/: brains/ForceManager.cpp, brains/ForceManager.hpp, |
3768 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
3769 |
|
|
brains/SimInfo.hpp, primitives/Molecule.cpp, |
3770 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp: refactory, |
3771 |
|
|
refactory, refactory |
3772 |
|
|
|
3773 |
gezelter |
2199 |
2004-11-12 17:43 tim |
3774 |
tim |
1779 |
|
3775 |
|
|
* src/utils/: StreamTokenizer.cpp, StringTokenizer.hpp, |
3776 |
|
|
StringTokenizer.cpp: bug fix in hasMoreTokens |
3777 |
|
|
|
3778 |
gezelter |
2199 |
2004-11-12 17:28 tim |
3779 |
tim |
1779 |
|
3780 |
|
|
* src/utils/StringTokenizer.cpp: file StringTokenizer.cpp was |
3781 |
|
|
initially added on branch new_design. |
3782 |
|
|
|
3783 |
gezelter |
2199 |
2004-11-12 17:28 tim |
3784 |
tim |
1779 |
|
3785 |
|
|
* src/utils/: StringTokenizer.cpp, StringTokenizer.hpp: adding |
3786 |
|
|
StringUtils, a c-style strtok like class, need unit test |
3787 |
|
|
|
3788 |
gezelter |
2199 |
2004-11-12 12:40 tim |
3789 |
tim |
1779 |
|
3790 |
|
|
* src/: UseTheForce/ForceField.cpp, UseTheForce/ForceField.hpp, |
3791 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
3792 |
|
|
brains/SimInfo.hpp: SimCreator and SimInfo are ready for unit test |
3793 |
|
|
|
3794 |
gezelter |
2199 |
2004-11-12 02:05 tim |
3795 |
tim |
1779 |
|
3796 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
3797 |
|
|
primitives/CutoffGroup.hpp, primitives/Molecule.cpp: |
3798 |
|
|
MoleculeCreator forget to create CutoffGroups for free atoms |
3799 |
|
|
|
3800 |
gezelter |
2199 |
2004-11-12 01:19 tim |
3801 |
tim |
1779 |
|
3802 |
|
|
* src/: brains/MoleculeCreator.cpp, brains/SimCreator.cpp, |
3803 |
|
|
brains/SimCreator.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
3804 |
|
|
brains/SimSnapshotManager.cpp, brains/SimSnapshotManager.hpp, |
3805 |
|
|
io/parse_me.h, primitives/Molecule.cpp, primitives/Molecule.hpp: |
3806 |
|
|
OOPSE = Object-Obfuscated Parallel Simulation Engine |
3807 |
|
|
|
3808 |
gezelter |
2199 |
2004-11-11 16:48 chrisfen |
3809 |
tim |
1779 |
|
3810 |
|
|
* samples/water/tip3p_ice/tp3.md: working sample |
3811 |
|
|
|
3812 |
gezelter |
2199 |
2004-11-11 16:47 chrisfen |
3813 |
tim |
1779 |
|
3814 |
|
|
* src/restraints/Restraints.cpp: working towards parallel |
3815 |
|
|
restraints |
3816 |
|
|
|
3817 |
gezelter |
2199 |
2004-11-11 16:47 chrisfen |
3818 |
tim |
1779 |
|
3819 |
|
|
* src/integrators/Integrator.cpp: Commented out some write |
3820 |
|
|
statements |
3821 |
|
|
|
3822 |
gezelter |
2199 |
2004-11-11 16:46 chrisfen |
3823 |
tim |
1779 |
|
3824 |
|
|
* src/UseTheForce/: Shapes_FF.cpp, doForces.F90: Got rid of some |
3825 |
|
|
write statements |
3826 |
|
|
|
3827 |
gezelter |
2199 |
2004-11-11 16:46 chrisfen |
3828 |
tim |
1779 |
|
3829 |
|
|
* samples/water/tip3p_ice/tp3.md: Fun with ice |
3830 |
|
|
|
3831 |
gezelter |
2199 |
2004-11-11 11:41 tim |
3832 |
tim |
1779 |
|
3833 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
3834 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
3835 |
|
|
brains/SnapShot.cpp, brains/Snapshot.hpp, brains/fSimulation.h, |
3836 |
|
|
brains/mpiSimulation.hpp, io/DumpWriter.cpp, io/StatWriter.cpp, |
3837 |
|
|
io/StatWriter.hpp, utils/Utility.hpp: add Snapshot.cpp, remove |
3838 |
|
|
useless mpiSimulation |
3839 |
|
|
|
3840 |
gezelter |
2199 |
2004-11-11 11:41 tim |
3841 |
tim |
1779 |
|
3842 |
|
|
* src/brains/SnapShot.cpp: file SnapShot.cpp was initially added on |
3843 |
|
|
branch new_design. |
3844 |
|
|
|
3845 |
gezelter |
2199 |
2004-11-10 17:50 tim |
3846 |
tim |
1779 |
|
3847 |
|
|
* src/: brains/ForceManager.cpp, brains/SimInfo.cpp, |
3848 |
|
|
brains/SimInfo.hpp, brains/Stats.hpp, brains/mpiSimulation.hpp, |
3849 |
|
|
integrators/NVE.cpp, io/StatWriter.cpp: more work on SimInfo |
3850 |
|
|
|
3851 |
gezelter |
2199 |
2004-11-10 17:01 tim |
3852 |
tim |
1779 |
|
3853 |
|
|
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
3854 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp, brains/SimSetup.cpp, |
3855 |
|
|
brains/Stats.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
3856 |
|
|
brains/mpiSimulation.hpp, integrators/VelocityVerletIntegrator.cpp, |
3857 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
3858 |
|
|
io/StatWriter.hpp, math/randomSPRNG.cpp, primitives/Molecule.hpp, |
3859 |
|
|
visitors/AtomVisitor.cpp: another painful day (1) SimCreator, |
3860 |
|
|
SimInfo, mpiSimulation (2) DumpReader, DumpWriter (InitializeFrom |
3861 |
|
|
File will be removed) (3) ForceField (at least LJ) and BondType, |
3862 |
|
|
BendType, TorsionType (4)Integrator (5)oopse.cpp (6)visitors & |
3863 |
|
|
Dump2XYZ (7)SimpleBuilder (8)Constraint & ZConstraint |
3864 |
|
|
|
3865 |
gezelter |
2199 |
2004-11-10 09:52 tim |
3866 |
tim |
1779 |
|
3867 |
|
|
* src/: brains/mpiSimulation.cpp, io/StatWriter.hpp: add a |
3868 |
|
|
configurable StatWriter |
3869 |
|
|
|
3870 |
gezelter |
2199 |
2004-11-10 09:52 tim |
3871 |
tim |
1779 |
|
3872 |
|
|
* src/io/StatWriter.hpp: file StatWriter.hpp was initially added on |
3873 |
|
|
branch new_design. |
3874 |
|
|
|
3875 |
gezelter |
2199 |
2004-11-09 21:58 tim |
3876 |
tim |
1779 |
|
3877 |
|
|
* src/brains/: mpiSimulation.cpp, mpiSimulation.hpp: mpiSimulation |
3878 |
|
|
in progress |
3879 |
|
|
|
3880 |
gezelter |
2199 |
2004-11-09 18:11 tim |
3881 |
tim |
1779 |
|
3882 |
tim |
2116 |
* src/brains/ForceManager.cpp: file ForceManager.cpp was initially |
3883 |
|
|
added on branch new_design. |
3884 |
|
|
|
3885 |
gezelter |
2199 |
2004-11-09 18:11 tim |
3886 |
tim |
2116 |
|
3887 |
|
|
* src/integrators/VelocityVerletIntegrator.cpp: file |
3888 |
|
|
VelocityVerletIntegrator.cpp was initially added on branch |
3889 |
|
|
new_design. |
3890 |
|
|
|
3891 |
gezelter |
2199 |
2004-11-09 18:11 tim |
3892 |
tim |
2116 |
|
3893 |
tim |
1779 |
* src/: UseTheForce/mpiComponentPlan.h, brains/ForceManager.cpp, |
3894 |
|
|
brains/ForceManager.hpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
3895 |
|
|
brains/Stats.hpp, brains/Thermo.cpp, brains/mpiSimulation.cpp, |
3896 |
|
|
brains/mpiSimulation.hpp, integrators/Integrator.hpp, |
3897 |
|
|
integrators/NVE.cpp, integrators/VelocityVerletIntegrator.cpp, |
3898 |
|
|
integrators/VelocityVerletIntegrator.hpp: adding ForceManager |
3899 |
|
|
|
3900 |
gezelter |
2199 |
2004-11-09 18:11 tim |
3901 |
tim |
1779 |
|
3902 |
|
|
* src/brains/ForceManager.hpp: file ForceManager.hpp was initially |
3903 |
|
|
added on branch new_design. |
3904 |
|
|
|
3905 |
gezelter |
2199 |
2004-11-09 18:11 tim |
3906 |
tim |
1779 |
|
3907 |
|
|
* src/integrators/NVE.cpp: file NVE.cpp was initially added on |
3908 |
|
|
branch new_design. |
3909 |
|
|
|
3910 |
gezelter |
2199 |
2004-11-08 20:08 tim |
3911 |
tim |
2102 |
|
3912 |
tim |
1779 |
* src/integrators/VelocityVerletIntegrator.hpp: file |
3913 |
|
|
VelocityVerletIntegrator.hpp was initially added on branch |
3914 |
|
|
new_design. |
3915 |
|
|
|
3916 |
gezelter |
2199 |
2004-11-08 20:08 tim |
3917 |
tim |
1779 |
|
3918 |
tim |
2116 |
* src/integrators/NVE.hpp: file NVE.hpp was initially added on |
3919 |
|
|
branch new_design. |
3920 |
|
|
|
3921 |
gezelter |
2199 |
2004-11-08 20:08 tim |
3922 |
tim |
2116 |
|
3923 |
tim |
1779 |
* src/: brains/Exclude.hpp, brains/Stats.hpp, |
3924 |
|
|
integrators/Integrator.hpp, integrators/NVE.hpp, |
3925 |
|
|
integrators/VelocityVerletIntegrator.hpp, io/StatWriter.cpp, |
3926 |
|
|
utils/TypeContainer.hpp: More to break |
3927 |
|
|
|
3928 |
gezelter |
2199 |
2004-11-06 00:21 tim |
3929 |
tim |
2102 |
|
3930 |
tim |
1779 |
* src/utils/TypeContainer.hpp: file TypeContainer.hpp was initially |
3931 |
|
|
added on branch new_design. |
3932 |
|
|
|
3933 |
gezelter |
2199 |
2004-11-06 00:21 tim |
3934 |
tim |
1779 |
|
3935 |
|
|
* src/: brains/SimCreator.hpp, UseTheForce/ForceField.cpp, |
3936 |
|
|
UseTheForce/ForceField.hpp, io/basic_ifstrstream.hpp, |
3937 |
|
|
utils/TypeContainer.hpp, utils/next_combination.hpp: adding |
3938 |
|
|
ForceField and TypeContainer classes |
3939 |
|
|
|
3940 |
gezelter |
2199 |
2004-11-05 18:38 tim |
3941 |
tim |
1779 |
|
3942 |
tim |
2116 |
* src/brains/MoleculeCreator.cpp: file MoleculeCreator.cpp was |
3943 |
|
|
initially added on branch new_design. |
3944 |
|
|
|
3945 |
gezelter |
2199 |
2004-11-05 18:38 tim |
3946 |
tim |
2116 |
|
3947 |
tim |
1779 |
* src/brains/MoleculeCreator.hpp: file MoleculeCreator.hpp was |
3948 |
|
|
initially added on branch new_design. |
3949 |
|
|
|
3950 |
gezelter |
2199 |
2004-11-05 18:38 tim |
3951 |
tim |
1779 |
|
3952 |
|
|
* src/: brains/Exclude.cpp, brains/Exclude.hpp, |
3953 |
|
|
brains/MoleculeCreator.cpp, brains/MoleculeCreator.hpp, |
3954 |
|
|
brains/SimCreator.cpp, brains/SimCreator.hpp, brains/SimInfo.cpp, |
3955 |
|
|
brains/SimInfo.hpp, primitives/Molecule.hpp, |
3956 |
|
|
utils/LocalndexManager.hpp: Fix Exclude class etc. |
3957 |
|
|
|
3958 |
gezelter |
2199 |
2004-11-05 16:45 chrisfen |
3959 |
tim |
2102 |
|
3960 |
tim |
1779 |
* src/: applications/dump2Xyz/Dump2XYZ.cpp, |
3961 |
|
|
visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: Added the |
3962 |
|
|
linear visitor |
3963 |
|
|
|
3964 |
gezelter |
2199 |
2004-11-05 16:04 chrisfen |
3965 |
tim |
1779 |
|
3966 |
|
|
* src/UseTheForce/DarkSide/shapes.F90: current status of the |
3967 |
|
|
debugging process |
3968 |
|
|
|
3969 |
gezelter |
2199 |
2004-11-05 16:04 chrisfen |
3970 |
tim |
1779 |
|
3971 |
|
|
* make/Makefile.in: included visitors and minimizer |
3972 |
|
|
|
3973 |
gezelter |
2199 |
2004-11-05 16:03 chrisfen |
3974 |
tim |
1779 |
|
3975 |
|
|
* ChangeLog: new changes |
3976 |
|
|
|
3977 |
gezelter |
2199 |
2004-11-04 21:56 tim |
3978 |
tim |
1701 |
|
3979 |
chrisfen |
1714 |
* src/: brains/SimCreator.cpp, brains/SimCreator.hpp, |
3980 |
|
|
primitives/Molecule.hpp: Pain...... |
3981 |
tim |
1712 |
|
3982 |
gezelter |
2199 |
2004-11-04 15:55 tim |
3983 |
chrisfen |
1714 |
|
3984 |
|
|
* ChangeLog, make/Makefile.in, src/brains/SimCreator.cpp, |
3985 |
|
|
src/brains/SimCreator.hpp, src/brains/SimInfo.hpp, |
3986 |
|
|
src/brains/Stats.hpp: time to break SimSetup |
3987 |
|
|
|
3988 |
gezelter |
2199 |
2004-11-04 15:51 gezelter |
3989 |
chrisfen |
1714 |
|
3990 |
|
|
* src/UseTheForce/: ForceField.cpp, ForceField.hpp: added new |
3991 |
|
|
classes in progress |
3992 |
|
|
|
3993 |
gezelter |
2199 |
2004-11-04 14:48 tim |
3994 |
tim |
1712 |
|
3995 |
|
|
* src/brains/Stats.cpp: file Stats.cpp was initially added on |
3996 |
tim |
1701 |
branch new_design. |
3997 |
|
|
|
3998 |
gezelter |
2199 |
2004-11-04 14:48 tim |
3999 |
tim |
1712 |
|
4000 |
|
|
* src/brains/Stats.hpp: file Stats.hpp was initially added on |
4001 |
|
|
branch new_design. |
4002 |
|
|
|
4003 |
gezelter |
2199 |
2004-11-04 14:48 tim |
4004 |
tim |
1712 |
|
4005 |
tim |
2116 |
* src/brains/: SimInfo.cpp, SimInfo.hpp, SimModel.cpp, |
4006 |
|
|
SimModel.hpp, Snapshot.hpp, Stats.cpp, Stats.hpp: adding Stats |
4007 |
|
|
class |
4008 |
|
|
|
4009 |
gezelter |
2199 |
2004-11-04 11:22 gezelter |
4010 |
tim |
2116 |
|
4011 |
tim |
1712 |
* src/primitives/: DirectionalAtom.cpp, DirectionalAtom.hpp, |
4012 |
|
|
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp: isLinear and |
4013 |
|
|
linearAxis are virtual in StuntDouble, but are implemented by |
4014 |
|
|
DirectionalAtom and RigidBody In StuntDouble, they should return |
4015 |
|
|
false and "-1" but there should be logic to figure them out in the |
4016 |
|
|
other two classes |
4017 |
|
|
|
4018 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
4019 |
tim |
1712 |
|
4020 |
|
|
* src/: brains/ForceFields.cpp, integrators/Integrator.cpp: Don't |
4021 |
|
|
remember what I did |
4022 |
|
|
|
4023 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
4024 |
tim |
1712 |
|
4025 |
|
|
* src/UseTheForce/DarkSide/shapes.F90: Breaky Breaky |
4026 |
|
|
|
4027 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
4028 |
tim |
1712 |
|
4029 |
|
|
* src/UseTheForce/: DUFF.cpp, WATER.cpp, doForces.F90: fixed useXXX |
4030 |
|
|
in the entry_plug so that it only is set if the atoms really are in |
4031 |
|
|
the simulation |
4032 |
|
|
|
4033 |
gezelter |
2199 |
2004-11-04 11:20 gezelter |
4034 |
tim |
1712 |
|
4035 |
|
|
* samples/water/ssd/ssd.md: testing force fields |
4036 |
|
|
|
4037 |
gezelter |
2199 |
2004-11-04 11:19 gezelter |
4038 |
tim |
1712 |
|
4039 |
|
|
* samples/shape/linear.in: testing shapes |
4040 |
|
|
|
4041 |
gezelter |
2199 |
2004-11-03 14:56 tim |
4042 |
tim |
1712 |
|
4043 |
|
|
* src/brains/: SimCreator.cpp, SimCreator.hpp: Adding SimCreator |
4044 |
|
|
class(similar as SimSetup) |
4045 |
|
|
|
4046 |
gezelter |
2199 |
2004-11-03 14:56 tim |
4047 |
tim |
1712 |
|
4048 |
|
|
* src/brains/SimCreator.hpp: file SimCreator.hpp was initially |
4049 |
|
|
added on branch new_design. |
4050 |
|
|
|
4051 |
gezelter |
2199 |
2004-11-03 14:56 tim |
4052 |
chrisfen |
1714 |
|
4053 |
|
|
* src/brains/SimCreator.cpp: file SimCreator.cpp was initially |
4054 |
|
|
added on branch new_design. |
4055 |
|
|
|
4056 |
gezelter |
2199 |
2004-11-03 13:00 tim |
4057 |
tim |
1712 |
|
4058 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
4059 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/LJFF.cpp, |
4060 |
|
|
UseTheForce/Shapes_FF.cpp, UseTheForce/WATER.cpp, |
4061 |
|
|
brains/DataStorage.hpp, primitives/Atom.hpp, |
4062 |
|
|
primitives/DirectionalAtom.hpp, restraints/Restraints.hpp, |
4063 |
|
|
visitors/BaseVisitor.hpp, visitors/ZconsVisitor.cpp: ForceFiled get |
4064 |
|
|
compiled. Still a long way to go ...... |
4065 |
|
|
|
4066 |
gezelter |
2199 |
2004-11-03 11:08 tim |
4067 |
tim |
1712 |
|
4068 |
|
|
* ChangeLog, src/brains/SimInfo.cpp, src/brains/SimInfo.hpp, |
4069 |
|
|
src/constraints/ZConstraint.cpp, src/integrators/NPT.cpp, |
4070 |
|
|
src/integrators/NPTf.cpp, src/integrators/NPTi.cpp, |
4071 |
|
|
src/integrators/NPTxyz.cpp, src/integrators/NVT.cpp, |
4072 |
|
|
src/io/ZConsReader.cpp, src/primitives/Bend.cpp, |
4073 |
|
|
src/primitives/Bond.cpp, src/primitives/GhostBend.cpp, |
4074 |
|
|
src/primitives/Molecule.cpp, src/primitives/Molecule.hpp, |
4075 |
|
|
src/primitives/SRI.hpp, src/primitives/StuntDouble.cpp, |
4076 |
|
|
src/primitives/StuntDouble.hpp, src/primitives/Torsion.cpp, |
4077 |
|
|
src/utils/GenericData.hpp, src/visitors/AtomVisitor.cpp, |
4078 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/RigidBodyVisitor.cpp, |
4079 |
|
|
src/visitors/ZconsVisitor.cpp, test/utils/Makefile: mess up ...... |
4080 |
|
|
|
4081 |
gezelter |
2199 |
2004-11-02 17:41 tim |
4082 |
tim |
1712 |
|
4083 |
tim |
2116 |
* src/: brains/Migrator.hpp, brains/SimModel.cpp, |
4084 |
|
|
utils/LocalndexManager.hpp: Adding LocalIndexManager and Migrator. |
4085 |
|
|
Need unit test |
4086 |
chrisfen |
1714 |
|
4087 |
gezelter |
2199 |
2004-11-02 17:41 tim |
4088 |
chrisfen |
1714 |
|
4089 |
tim |
1712 |
* src/utils/LocalndexManager.hpp: file LocalndexManager.hpp was |
4090 |
|
|
initially added on branch new_design. |
4091 |
|
|
|
4092 |
gezelter |
2199 |
2004-11-02 17:41 tim |
4093 |
tim |
1712 |
|
4094 |
tim |
2116 |
* src/brains/Migrator.hpp: file Migrator.hpp was initially added on |
4095 |
|
|
branch new_design. |
4096 |
tim |
1712 |
|
4097 |
gezelter |
2199 |
2004-11-02 11:59 tim |
4098 |
tim |
1712 |
|
4099 |
tim |
2116 |
* src/brains/SimModel.cpp: file SimModel.cpp was initially added on |
4100 |
|
|
branch new_design. |
4101 |
|
|
|
4102 |
gezelter |
2199 |
2004-11-02 11:59 tim |
4103 |
tim |
2116 |
|
4104 |
tim |
2102 |
* src/brains/: SimModel.cpp, SimModel.hpp, SimSnapshotManager.cpp, |
4105 |
|
|
SimSnapshotManager.hpp: SimModel in progress |
4106 |
tim |
1712 |
|
4107 |
gezelter |
2199 |
2004-11-02 10:28 chrisfen |
4108 |
tim |
1701 |
|
4109 |
|
|
* src/: UseTheForce/DarkSide/shapes.F90, |
4110 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp: Shapes |
4111 |
|
|
looks like it's working |
4112 |
|
|
|
4113 |
gezelter |
2199 |
2004-11-02 10:27 tim |
4114 |
tim |
1701 |
|
4115 |
tim |
2116 |
* src/utils/MemoryUtils.hpp: adding MemoryUtils which provide some |
4116 |
|
|
functions for dealing with memory issue |
4117 |
|
|
|
4118 |
gezelter |
2199 |
2004-11-02 10:27 tim |
4119 |
tim |
2116 |
|
4120 |
tim |
2102 |
* src/utils/MemoryUtils.hpp: file MemoryUtils.hpp was initially |
4121 |
|
|
added on branch new_design. |
4122 |
tim |
1701 |
|
4123 |
gezelter |
2199 |
2004-11-02 10:23 tim |
4124 |
tim |
1701 |
|
4125 |
|
|
* src/: brains/SimModel.hpp, brains/Snapshot.hpp, |
4126 |
|
|
brains/SnapshotManager.hpp, primitives/Molecule.hpp: adding |
4127 |
|
|
SimModel(something similar as SimInfo) |
4128 |
|
|
|
4129 |
gezelter |
2199 |
2004-11-01 17:52 tim |
4130 |
tim |
1701 |
|
4131 |
|
|
* src/: applications/simpleBuilder/MoLocator.hpp, |
4132 |
|
|
applications/simpleBuilder/simpleBuilder.cpp, |
4133 |
|
|
brains/DataStorage.hpp, brains/ForceFields.cpp, |
4134 |
|
|
brains/Snapshot.hpp, brains/SnapshotManager.hpp, brains/Thermo.cpp, |
4135 |
|
|
constraints/ZConstraint.cpp, integrators/Integrator.cpp, |
4136 |
|
|
integrators/NPT.cpp, integrators/NVT.cpp, io/DumpWriter.cpp, |
4137 |
|
|
math/SquareMatrix3.hpp, math/Vector3.hpp, |
4138 |
|
|
minimizers/OOPSEMinimizer.cpp, primitives/Bend.hpp, |
4139 |
|
|
primitives/Bond.hpp, primitives/CutoffGroup.hpp, |
4140 |
|
|
primitives/Molecule.cpp, primitives/Molecule.hpp, |
4141 |
|
|
primitives/RigidBody.hpp, primitives/Torsion.hpp, |
4142 |
|
|
restraints/Restraints.cpp, types/TorsionType.hpp, |
4143 |
|
|
utils/PropertyMap.hpp, utils/StringTokenizer.hpp, |
4144 |
|
|
visitors/AtomVisitor.cpp, visitors/BaseVisitor.hpp, |
4145 |
|
|
visitors/RigidBodyVisitor.cpp: Molecule, Atom, DirectionalAtom, |
4146 |
|
|
RigidBody and StuntDouble classes get compiled |
4147 |
|
|
|
4148 |
gezelter |
2199 |
2004-11-01 16:40 tim |
4149 |
tim |
1701 |
|
4150 |
tim |
2116 |
* src/primitives/Torsion.hpp: file Torsion.hpp was initially added |
4151 |
|
|
on branch new_design. |
4152 |
|
|
|
4153 |
gezelter |
2199 |
2004-11-01 16:40 tim |
4154 |
tim |
2116 |
|
4155 |
tim |
2102 |
* src/primitives/Bend.hpp: file Bend.hpp was initially added on |
4156 |
|
|
branch new_design. |
4157 |
tim |
1701 |
|
4158 |
gezelter |
2199 |
2004-11-01 16:40 tim |
4159 |
tim |
1701 |
|
4160 |
|
|
* src/primitives/Bond.hpp: file Bond.hpp was initially added on |
4161 |
|
|
branch new_design. |
4162 |
|
|
|
4163 |
gezelter |
2199 |
2004-11-01 16:40 tim |
4164 |
tim |
1701 |
|
4165 |
tim |
2116 |
* src/primitives/: Bend.hpp, Bond.hpp, Torsion.hpp: add initial |
4166 |
|
|
version of Bond, Bend and Torsion. |
4167 |
tim |
1701 |
|
4168 |
gezelter |
2199 |
2004-11-01 16:37 tim |
4169 |
tim |
1701 |
|
4170 |
|
|
* src/types/BendType.hpp: file BendType.hpp was initially added on |
4171 |
|
|
branch new_design. |
4172 |
|
|
|
4173 |
gezelter |
2199 |
2004-11-01 16:37 tim |
4174 |
tim |
1701 |
|
4175 |
tim |
2116 |
* src/types/: BendType.hpp, BondType.hpp, TorsionType.hpp: adding |
4176 |
|
|
BondType, BendType, TorsionType |
4177 |
tim |
1701 |
|
4178 |
gezelter |
2199 |
2004-11-01 16:37 tim |
4179 |
tim |
1701 |
|
4180 |
|
|
* src/types/TorsionType.hpp: file TorsionType.hpp was initially |
4181 |
|
|
added on branch new_design. |
4182 |
|
|
|
4183 |
gezelter |
2199 |
2004-11-01 16:37 tim |
4184 |
tim |
1701 |
|
4185 |
tim |
2116 |
* src/types/BondType.hpp: file BondType.hpp was initially added on |
4186 |
|
|
branch new_design. |
4187 |
tim |
1701 |
|
4188 |
gezelter |
2199 |
2004-11-01 15:15 tim |
4189 |
tim |
1701 |
|
4190 |
|
|
* src/primitives/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
4191 |
|
|
CutoffGroup.hpp, DirectionalAtom.cpp, DirectionalAtom.hpp, |
4192 |
|
|
GhostBend.cpp, Makefile, Molecule.cpp, Molecule.hpp, RigidBody.cpp, |
4193 |
|
|
RigidBody.hpp, StuntDouble.cpp, StuntDouble.hpp, Torsion.cpp: |
4194 |
|
|
break, break and break..... |
4195 |
|
|
|
4196 |
gezelter |
2199 |
2004-11-01 14:57 tim |
4197 |
tim |
1701 |
|
4198 |
|
|
* test/brains/: Atom.cpp, DirectioanlAtom.cpp, DirectionalAtom.cpp, |
4199 |
|
|
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp, |
4200 |
|
|
StuntDouble.hpp: these core classes get compiled |
4201 |
|
|
|
4202 |
gezelter |
2199 |
2004-10-29 17:37 tim |
4203 |
tim |
1701 |
|
4204 |
|
|
* test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule |
4205 |
|
|
class |
4206 |
|
|
|
4207 |
gezelter |
2199 |
2004-10-29 17:28 chrisfen |
4208 |
tim |
1701 |
|
4209 |
|
|
* src/: UseTheForce/DarkSide/atype.F90, |
4210 |
|
|
UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp, |
4211 |
|
|
types/ShapeAtomType.cpp: still debugging |
4212 |
|
|
|
4213 |
gezelter |
2199 |
2004-10-29 17:28 chrisfen |
4214 |
tim |
1701 |
|
4215 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90: |
4216 |
|
|
shapes rcut calculator added |
4217 |
|
|
|
4218 |
gezelter |
2199 |
2004-10-29 17:27 chrisfen |
4219 |
tim |
1701 |
|
4220 |
|
|
* samples/shape/linear.md: shorter run |
4221 |
|
|
|
4222 |
gezelter |
2199 |
2004-10-29 15:54 tim |
4223 |
tim |
1701 |
|
4224 |
|
|
* test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class. |
4225 |
|
|
|
4226 |
gezelter |
2199 |
2004-10-29 11:22 tim |
4227 |
tim |
1701 |
|
4228 |
|
|
* test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp, |
4229 |
|
|
ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove |
4230 |
|
|
some deprecated files |
4231 |
|
|
|
4232 |
gezelter |
2199 |
2004-10-29 11:20 tim |
4233 |
tim |
1701 |
|
4234 |
|
|
* test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp, |
4235 |
|
|
DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp: |
4236 |
|
|
More painful reconstruction is coming !!! |
4237 |
|
|
|
4238 |
gezelter |
2199 |
2004-10-28 17:34 tim |
4239 |
tim |
1701 |
|
4240 |
|
|
* src/brains/DataStorage.hpp, src/utils/next_combination.hpp, |
4241 |
|
|
test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp, |
4242 |
|
|
test/brains/RigidBody.cpp, test/brains/RigidBody.hpp, |
4243 |
|
|
test/brains/StuntDouble.hpp: More work on StuntDouble, Atom, |
4244 |
|
|
DirectionalAtom and RigidBody |
4245 |
|
|
|
4246 |
gezelter |
2199 |
2004-10-28 17:26 tim |
4247 |
tim |
1701 |
|
4248 |
|
|
* ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp, |
4249 |
|
|
src/applications/simpleBuilder/MoLocator.cpp, |
4250 |
|
|
src/applications/simpleBuilder/Vector3d.hpp, |
4251 |
|
|
src/utils/GenericFactory.hpp, src/utils/next_combination.hpp: |
4252 |
|
|
remove old Vector3d.hpp from application/simpleBuilder |
4253 |
|
|
|
4254 |
gezelter |
2199 |
2004-10-28 16:42 tim |
4255 |
tim |
1701 |
|
4256 |
|
|
* src/utils/next_combination.hpp: Minor change in next_combination |
4257 |
|
|
|
4258 |
gezelter |
2199 |
2004-10-28 16:28 tim |
4259 |
tim |
1681 |
|
4260 |
|
|
* src/utils/next_combination.hpp, |
4261 |
|
|
test/utils/NextCombinationTestCase.cpp, |
4262 |
|
|
test/utils/ReplaceWildCardTestCase.cpp: Done with combination |
4263 |
|
|
|
4264 |
gezelter |
2199 |
2004-10-28 16:11 tim |
4265 |
tim |
1681 |
|
4266 |
|
|
* src/utils/next_combination.hpp: change documentation of |
4267 |
|
|
next_combination.hpp |
4268 |
|
|
|
4269 |
gezelter |
2199 |
2004-10-28 15:41 tim |
4270 |
tim |
1681 |
|
4271 |
|
|
* ChangeLog, src/utils/next_combination.hpp, |
4272 |
|
|
test/utils/NextCombinationTestCase.cpp, |
4273 |
|
|
test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working |
4274 |
|
|
|
4275 |
gezelter |
2199 |
2004-10-28 15:01 tim |
4276 |
tim |
1681 |
|
4277 |
|
|
* src/utils/next_combination.hpp: adding replace wildcard function |
4278 |
|
|
|
4279 |
gezelter |
2199 |
2004-10-28 14:33 tim |
4280 |
tim |
1681 |
|
4281 |
|
|
* src/utils/next_combination.hpp: Minor change |
4282 |
|
|
|
4283 |
gezelter |
2199 |
2004-10-28 14:06 tim |
4284 |
tim |
1677 |
|
4285 |
|
|
* ChangeLog, src/applications/simpleBuilder/MoLocator.hpp, |
4286 |
|
|
src/applications/simpleBuilder/simpleBuilder.cpp, |
4287 |
|
|
src/utils/next_combination.hpp, test/utils/Makefile, |
4288 |
|
|
test/utils/NextCombinationTestCase.cpp, |
4289 |
|
|
test/utils/ReplaceWildCardTestCase.cpp, |
4290 |
|
|
test/utils/next_combination.hpp: STL next_permutation like |
4291 |
|
|
next_combination is working |
4292 |
|
|
|
4293 |
gezelter |
2199 |
2004-10-28 12:22 chrisfen |
4294 |
tim |
1677 |
|
4295 |
|
|
* src/UseTheForce/WATER.cpp: fix of setDipoles |
4296 |
|
|
|
4297 |
gezelter |
2199 |
2004-10-28 12:20 gezelter |
4298 |
tim |
1677 |
|
4299 |
|
|
* src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the |
4300 |
|
|
shapeFile |
4301 |
|
|
|
4302 |
gezelter |
2199 |
2004-10-28 12:20 gezelter |
4303 |
tim |
1677 |
|
4304 |
|
|
* samples/shape/linear.md: forgot the orientation line |
4305 |
|
|
|
4306 |
gezelter |
2199 |
2004-10-28 11:56 gezelter |
4307 |
tim |
1677 |
|
4308 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
4309 |
|
|
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
4310 |
|
|
UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate |
4311 |
|
|
declaration foo |
4312 |
|
|
|
4313 |
gezelter |
2199 |
2004-10-28 11:55 gezelter |
4314 |
tim |
1677 |
|
4315 |
|
|
* samples/lipid/5x5.md: uncommented .in line |
4316 |
|
|
|
4317 |
gezelter |
2199 |
2004-10-28 10:42 tim |
4318 |
tim |
1677 |
|
4319 |
|
|
* test/utils/: Makefile, NextCombinationTestCase.cpp, |
4320 |
|
|
NextCombinationTestCase.hpp, next_combination.hpp: next_combination |
4321 |
|
|
in progress |
4322 |
|
|
|
4323 |
gezelter |
2199 |
2004-10-28 10:15 tim |
4324 |
tim |
1677 |
|
4325 |
|
|
* test/utils/: NextCombinationTestCase.cpp, |
4326 |
|
|
NextCombinationTestCase.hpp: adding next_combination test case |
4327 |
|
|
|
4328 |
gezelter |
2199 |
2004-10-28 10:02 tim |
4329 |
tim |
1677 |
|
4330 |
|
|
* test/utils/next_combination.hpp: STL Compatible combination |
4331 |
|
|
sequence generator |
4332 |
|
|
|
4333 |
gezelter |
2199 |
2004-10-28 01:23 tim |
4334 |
tim |
1677 |
|
4335 |
|
|
* test/utils/: GenerateCombination.hpp, |
4336 |
|
|
ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp |
4337 |
|
|
|
4338 |
gezelter |
2199 |
2004-10-28 01:16 tim |
4339 |
tim |
1677 |
|
4340 |
|
|
* test/utils/GenerateCombination.hpp: a STL next_permutaion like |
4341 |
|
|
next_combination function. |
4342 |
|
|
|
4343 |
gezelter |
2199 |
2004-10-27 22:27 tim |
4344 |
tim |
1677 |
|
4345 |
|
|
* test/utils/ReplaceWildCard.hpp: no message |
4346 |
|
|
|
4347 |
gezelter |
2199 |
2004-10-27 22:14 tim |
4348 |
tim |
1677 |
|
4349 |
|
|
* test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp: |
4350 |
|
|
ReplaceWildCard(recursive version) is working, need refactoring. An |
4351 |
|
|
iterative version is on the way |
4352 |
|
|
|
4353 |
gezelter |
2199 |
2004-10-27 21:28 tim |
4354 |
tim |
1677 |
|
4355 |
|
|
* test/utils/: Makefile, ReplaceWildCard.hpp, |
4356 |
|
|
ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress |
4357 |
|
|
|
4358 |
gezelter |
2199 |
2004-10-27 21:08 tim |
4359 |
tim |
1677 |
|
4360 |
|
|
* test/utils/: ReplaceWildCardTestCase.cpp, |
4361 |
|
|
ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard |
4362 |
|
|
|
4363 |
gezelter |
2199 |
2004-10-27 18:17 tim |
4364 |
tim |
1677 |
|
4365 |
|
|
* test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need |
4366 |
|
|
test |
4367 |
|
|
|
4368 |
gezelter |
2199 |
2004-10-27 01:25 tim |
4369 |
tim |
1677 |
|
4370 |
|
|
* src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild |
4371 |
|
|
char matching is on the way |
4372 |
|
|
|
4373 |
gezelter |
2199 |
2004-10-27 01:07 tim |
4374 |
tim |
1677 |
|
4375 |
|
|
* src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4 |
4376 |
|
|
|
4377 |
gezelter |
2199 |
2004-10-26 22:00 gezelter |
4378 |
tim |
1674 |
|
4379 |
|
|
* src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix |
4380 |
|
|
|
4381 |
gezelter |
2199 |
2004-10-26 21:20 gezelter |
4382 |
tim |
1674 |
|
4383 |
|
|
* src/UseTheForce/ForceFields.hpp: subclass foo |
4384 |
|
|
|
4385 |
gezelter |
2199 |
2004-10-26 21:16 gezelter |
4386 |
tim |
1674 |
|
4387 |
|
|
* src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* -> |
4388 |
|
|
string conversion |
4389 |
|
|
|
4390 |
gezelter |
2199 |
2004-10-26 19:01 gezelter |
4391 |
tim |
1674 |
|
4392 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
4393 |
|
|
UseTheForce/ForceFields.hpp, brains/SimSetup.cpp, |
4394 |
|
|
brains/SimSetup.hpp: char* -> string |
4395 |
|
|
|
4396 |
gezelter |
2199 |
2004-10-26 17:25 gezelter |
4397 |
tim |
1674 |
|
4398 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp, |
4399 |
|
|
Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp, |
4400 |
|
|
ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some |
4401 |
|
|
isXXX |
4402 |
|
|
|
4403 |
gezelter |
2199 |
2004-10-26 17:25 gezelter |
4404 |
tim |
1674 |
|
4405 |
|
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
4406 |
|
|
define name collision |
4407 |
|
|
|
4408 |
gezelter |
2199 |
2004-10-26 17:24 gezelter |
4409 |
tim |
1674 |
|
4410 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
4411 |
|
|
UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp, |
4412 |
|
|
UseTheForce/Makefile, UseTheForce/Shapes_FF.cpp, |
4413 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
4414 |
|
|
UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp: |
4415 |
|
|
forcefield refactoring for shapes |
4416 |
|
|
|
4417 |
gezelter |
2199 |
2004-10-26 17:24 gezelter |
4418 |
tim |
1677 |
|
4419 |
|
|
* samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape, |
4420 |
|
|
Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in, |
4421 |
|
|
linear.md, linear.shape, toluene.shape: adding sample shape |
4422 |
|
|
directory |
4423 |
|
|
|
4424 |
gezelter |
2199 |
2004-10-26 17:19 tim |
4425 |
tim |
1674 |
|
4426 |
|
|
* ChangeLog, src/brains/DataStorage.cpp, |
4427 |
|
|
src/brains/DataStorage.hpp, src/brains/Snapshot.hpp, |
4428 |
|
|
test/brains/DataStorageTestCase.cpp, |
4429 |
|
|
test/brains/DataStorageTestCase.hpp, test/brains/Makefile: |
4430 |
|
|
DataStorage passes unit test |
4431 |
|
|
|
4432 |
gezelter |
2199 |
2004-10-26 13:03 chrisfen |
4433 |
tim |
1674 |
|
4434 |
|
|
* src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h: |
4435 |
|
|
Changes to help advance shapes |
4436 |
|
|
|
4437 |
gezelter |
2199 |
2004-10-26 13:02 chrisfen |
4438 |
tim |
1674 |
|
4439 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to |
4440 |
|
|
Shapes force field reader |
4441 |
|
|
|
4442 |
gezelter |
2199 |
2004-10-26 12:28 tim |
4443 |
tim |
1674 |
|
4444 |
|
|
* src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and |
4445 |
|
|
SnapshotTestCase in progress |
4446 |
|
|
|
4447 |
gezelter |
2199 |
2004-10-25 17:46 tim |
4448 |
tim |
1648 |
|
4449 |
|
|
* ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
4450 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
4451 |
|
|
src/math/Vector3.hpp, test/brains/StuntDouble.hpp, |
4452 |
|
|
test/math/RectMatrixTestCase.cpp, test/math/Vector3TestCase.cpp, |
4453 |
|
|
test/math/VectorTestCase.cpp: add getArray function to RectMatrix |
4454 |
|
|
and Vector classes |
4455 |
|
|
|
4456 |
gezelter |
2199 |
2004-10-25 12:03 tim |
4457 |
tim |
1644 |
|
4458 |
|
|
* ChangeLog, src/utils/GenericFactory.hpp, |
4459 |
|
|
test/utils/GenericFactoryTestCase.cpp, |
4460 |
|
|
test/utils/GenericFactoryTestCase.hpp, test/utils/Makefile: adding |
4461 |
|
|
GenericFactory Test Case. GenericFactory now can bed used to creat |
4462 |
|
|
ForcefieldFactory and IntegratorFactory etc. |
4463 |
|
|
|
4464 |
gezelter |
2199 |
2004-10-24 23:08 tim |
4465 |
tim |
1644 |
|
4466 |
|
|
* src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp, |
4467 |
|
|
brains/SimSnapshotManager.hpp, brains/Snapshot.hpp, |
4468 |
|
|
brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes |
4469 |
|
|
get reconstructed |
4470 |
|
|
|
4471 |
gezelter |
2199 |
2004-10-24 02:55 tim |
4472 |
tim |
1644 |
|
4473 |
|
|
* src/utils/GenericFactory.hpp: GenericFactory pass unit test |
4474 |
|
|
|
4475 |
gezelter |
2199 |
2004-10-23 18:09 tim |
4476 |
tim |
1644 |
|
4477 |
|
|
* test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp, |
4478 |
|
|
StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp, |
4479 |
|
|
RigidBody.cpp: Refactoring in progress |
4480 |
|
|
|
4481 |
gezelter |
2199 |
2004-10-22 18:09 tim |
4482 |
tim |
1643 |
|
4483 |
|
|
* ChangeLog, src/brains/Snapshot.hpp, |
4484 |
|
|
src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp, |
4485 |
|
|
test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp, |
4486 |
|
|
test/brains/StuntDouble.hpp: more work in Snapshot |
4487 |
|
|
|
4488 |
gezelter |
2199 |
2004-10-22 17:59 chrisfen |
4489 |
tim |
1643 |
|
4490 |
|
|
* src/: UseTheForce/LJFF.cpp, |
4491 |
|
|
UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear |
4492 |
|
|
god! It runs and conserves energy! |
4493 |
|
|
|
4494 |
gezelter |
2199 |
2004-10-22 17:54 chrisfen |
4495 |
tim |
1643 |
|
4496 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY |
4497 |
|
|
|
4498 |
gezelter |
2199 |
2004-10-22 17:53 chrisfen |
4499 |
tim |
1643 |
|
4500 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
4501 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
4502 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
4503 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey |
4504 |
|
|
breakey |
4505 |
|
|
|
4506 |
gezelter |
2199 |
2004-10-22 17:53 chrisfen |
4507 |
tim |
1643 |
|
4508 |
|
|
* make/Makefile.in: compiler flags |
4509 |
|
|
|
4510 |
gezelter |
2199 |
2004-10-22 16:20 gezelter |
4511 |
tim |
1643 |
|
4512 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
4513 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/doForces.F90, |
4514 |
|
|
brains/fSimulation.h, types/AtomType.hpp, |
4515 |
|
|
types/DirectionalAtomType.hpp: fixey fixey |
4516 |
|
|
|
4517 |
gezelter |
2199 |
2004-10-22 15:22 gezelter |
4518 |
tim |
1643 |
|
4519 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h, |
4520 |
|
|
charge.F90, charge_interface.h, dipole.F90, dipole_interface.h, |
4521 |
|
|
lj_interface.h, shapes.F90, simulation.F90: Added un-busticated |
4522 |
|
|
fortran files and c/Fortran interfaces |
4523 |
|
|
|
4524 |
gezelter |
2199 |
2004-10-22 15:21 gezelter |
4525 |
tim |
1643 |
|
4526 |
|
|
* src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h, |
4527 |
|
|
DirectionalAtomType.hpp, Makefile: More on AtomType and |
4528 |
|
|
DirectionalAtomType |
4529 |
|
|
|
4530 |
gezelter |
2199 |
2004-10-22 09:47 gezelter |
4531 |
tim |
1639 |
|
4532 |
|
|
* src/types/AtomType.hpp: Adding AtomType |
4533 |
|
|
|
4534 |
gezelter |
2199 |
2004-10-21 16:31 tim |
4535 |
tim |
1639 |
|
4536 |
|
|
* ChangeLog, src/brains/Snapshot.hpp, |
4537 |
|
|
src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp, |
4538 |
|
|
src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
4539 |
|
|
src/math/Vector.hpp, src/math/Vector3.hpp, |
4540 |
|
|
test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp: |
4541 |
|
|
Snapshot and SnapshotManager in progress |
4542 |
|
|
|
4543 |
gezelter |
2199 |
2004-10-21 16:30 tim |
4544 |
tim |
1639 |
|
4545 |
|
|
* test/brains/: BrainsTest.cpp, Makefile, |
4546 |
|
|
SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp, |
4547 |
|
|
SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for |
4548 |
|
|
Snapshot and snapshotManager. |
4549 |
|
|
|
4550 |
gezelter |
2199 |
2004-10-21 15:15 gezelter |
4551 |
tim |
1630 |
|
4552 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
4553 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
4554 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp, |
4555 |
|
|
UseTheForce/WATER.cpp, UseTheForce/doForces.F90, |
4556 |
|
|
UseTheForce/doForces_interface.h, UseTheForce/fForceField.h, |
4557 |
|
|
UseTheForce/DarkSide/LJ.F90, UseTheForce/DarkSide/lj_interface.h, |
4558 |
|
|
brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky. |
4559 |
|
|
Fixey Fixey. |
4560 |
|
|
|
4561 |
gezelter |
2199 |
2004-10-21 11:32 tim |
4562 |
tim |
1630 |
|
4563 |
|
|
* src/utils/GenericData.cpp, src/utils/Makefile, |
4564 |
|
|
test/utils/Makefile, test/utils/UtilTest: remove some junk files |
4565 |
|
|
|
4566 |
gezelter |
2199 |
2004-10-21 11:24 tim |
4567 |
tim |
1630 |
|
4568 |
|
|
* test/utils/GenericData.hpp: remove backup of GenericData.hpp |
4569 |
|
|
|
4570 |
gezelter |
2199 |
2004-10-21 11:22 tim |
4571 |
tim |
1630 |
|
4572 |
|
|
* ChangeLog, src/brains/SimSetup.cpp, |
4573 |
|
|
src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp, |
4574 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
4575 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
4576 |
|
|
src/integrators/NVT.cpp, src/io/DumpReader.cpp, |
4577 |
|
|
src/io/InitializeFromFile.cpp, src/io/ZConsReader.cpp, |
4578 |
|
|
src/io/ZConsWriter.hpp, src/primitives/StuntDouble.hpp, |
4579 |
|
|
src/utils/GenericData.cpp, src/utils/GenericData.hpp, |
4580 |
|
|
src/visitors/AtomData.hpp, src/visitors/AtomVisitor.cpp, |
4581 |
|
|
src/visitors/AtomVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
4582 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/OtherVisitor.cpp, |
4583 |
|
|
src/visitors/OtherVisitor.hpp, src/visitors/RigidBodyVisitor.cpp, |
4584 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
4585 |
|
|
src/visitors/ZconsVisitor.hpp: replace old GebericData with new |
4586 |
|
|
GenericData |
4587 |
|
|
|
4588 |
gezelter |
2199 |
2004-10-21 10:25 chuckv |
4589 |
tim |
1630 |
|
4590 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj |
4591 |
|
|
module. |
4592 |
|
|
|
4593 |
gezelter |
2199 |
2004-10-21 10:24 chuckv |
4594 |
tim |
1630 |
|
4595 |
|
|
* src/UseTheForce/DarkSide/lj_interface.h: Added interface for |
4596 |
|
|
fortran lj module. |
4597 |
|
|
|
4598 |
gezelter |
2199 |
2004-10-20 17:54 tim |
4599 |
tim |
1625 |
|
4600 |
|
|
* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
4601 |
|
|
test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
4602 |
|
|
test/utils/PropertyMapTestCase.cpp, |
4603 |
|
|
test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
4604 |
|
|
GenericData and PropertyMap pass unit test. |
4605 |
|
|
|
4606 |
gezelter |
2199 |
2004-10-20 16:52 gezelter |
4607 |
tim |
1622 |
|
4608 |
|
|
* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
4609 |
|
|
DarkSide/sticky_interface.h: fixed a fortran name problem |
4610 |
|
|
|
4611 |
gezelter |
2199 |
2004-10-20 16:38 tim |
4612 |
tim |
1622 |
|
4613 |
|
|
* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
4614 |
|
|
GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
4615 |
|
|
UtilTest, UtilTest.cpp: adding generic data test case |
4616 |
|
|
|
4617 |
gezelter |
2199 |
2004-10-20 16:16 chuckv |
4618 |
tim |
1622 |
|
4619 |
|
|
* configure, ac-tools/aclocal.m4, |
4620 |
|
|
src/UseTheForce/DarkSide/Makefile, |
4621 |
|
|
src/UseTheForce/DarkSide/mpiSimulation.F90, |
4622 |
|
|
src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
4623 |
|
|
src/UseTheForce/DarkSide/simParallel.F90, |
4624 |
|
|
src/UseTheForce/DarkSide/simParallel_interface.h, |
4625 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
4626 |
|
|
Fortran/C++ interface de-obfuscation project appears to be |
4627 |
|
|
complete! Woo hoo! |
4628 |
|
|
|
4629 |
gezelter |
2199 |
2004-10-20 15:47 chuckv |
4630 |
tim |
1622 |
|
4631 |
|
|
* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
4632 |
|
|
fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
4633 |
|
|
continues |
4634 |
|
|
|
4635 |
gezelter |
2199 |
2004-10-20 15:46 chuckv |
4636 |
tim |
1622 |
|
4637 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
4638 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
4639 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
4640 |
|
|
UseTheForce/doForces_interface.h, |
4641 |
|
|
UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
4642 |
|
|
UseTheForce/DarkSide/atype_interface.h, |
4643 |
|
|
UseTheForce/DarkSide/eam_interface.h, |
4644 |
|
|
UseTheForce/DarkSide/gb_interface.h, |
4645 |
|
|
UseTheForce/DarkSide/mpiSimulation_interface.h, |
4646 |
|
|
UseTheForce/DarkSide/shapes_interface.h, |
4647 |
|
|
UseTheForce/DarkSide/simulation_interface.h, |
4648 |
|
|
UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
4649 |
|
|
brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
4650 |
|
|
de-obfuscation project (It is a very long story) |
4651 |
|
|
|
4652 |
gezelter |
2199 |
2004-10-20 13:07 tim |
4653 |
tim |
1622 |
|
4654 |
|
|
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
4655 |
|
|
test/math/SquareMatrix3TestCase.cpp, |
4656 |
|
|
test/math/SquareMatrixTestCase.cpp, |
4657 |
|
|
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
4658 |
|
|
|
4659 |
gezelter |
2199 |
2004-10-20 00:52 tim |
4660 |
tim |
1616 |
|
4661 |
|
|
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
4662 |
|
|
SnapshotManager in design phase |
4663 |
|
|
|
4664 |
gezelter |
2199 |
2004-10-19 23:54 gezelter |
4665 |
tim |
1616 |
|
4666 |
|
|
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
4667 |
|
|
problem prevented linking |
4668 |
|
|
|
4669 |
gezelter |
2199 |
2004-10-19 23:54 gezelter |
4670 |
tim |
1616 |
|
4671 |
|
|
* src/UseTheForce/Shapes_FF.cpp: fixed include |
4672 |
|
|
|
4673 |
gezelter |
2199 |
2004-10-19 23:26 gezelter |
4674 |
tim |
1616 |
|
4675 |
|
|
* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
4676 |
|
|
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
4677 |
|
|
more fortran name mangling |
4678 |
|
|
|
4679 |
gezelter |
2199 |
2004-10-19 23:23 gezelter |
4680 |
tim |
1616 |
|
4681 |
|
|
* src/profiling/timing.F90: yet more fortran renaming |
4682 |
|
|
|
4683 |
gezelter |
2199 |
2004-10-19 23:19 gezelter |
4684 |
tim |
1616 |
|
4685 |
|
|
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
4686 |
|
|
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
4687 |
|
|
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
4688 |
|
|
wrappers.F90: Fortran name cleanup continues |
4689 |
|
|
|
4690 |
gezelter |
2199 |
2004-10-19 23:12 gezelter |
4691 |
tim |
1616 |
|
4692 |
|
|
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
4693 |
|
|
broken fortran stuff |
4694 |
|
|
|
4695 |
gezelter |
2199 |
2004-10-19 23:02 gezelter |
4696 |
tim |
1616 |
|
4697 |
|
|
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
4698 |
|
|
atype_interface.h, atype_module.F90, atype_module_interface.h, |
4699 |
|
|
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
4700 |
|
|
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
4701 |
|
|
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
4702 |
|
|
eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
4703 |
|
|
gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
4704 |
|
|
mpiSimulation_interface.h, mpiSimulation_module.F90, |
4705 |
|
|
mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
4706 |
|
|
shapes_interface.h, shapes_module.h, simulation.F90, |
4707 |
|
|
simulation_interface.h, simulation_module.F90, |
4708 |
|
|
simulation_module_interface.h, sticky.F90, sticky_interface.h, |
4709 |
|
|
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
4710 |
|
|
name sanity on the fortran side |
4711 |
|
|
|
4712 |
gezelter |
2199 |
2004-10-19 19:18 tim |
4713 |
tim |
1616 |
|
4714 |
|
|
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
4715 |
|
|
|
4716 |
gezelter |
2199 |
2004-10-19 18:01 tim |
4717 |
tim |
1616 |
|
4718 |
|
|
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
4719 |
|
|
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
4720 |
|
|
except diagonalize(), all of functions in math library pass the |
4721 |
|
|
test |
4722 |
|
|
|
4723 |
gezelter |
2199 |
2004-10-19 17:43 chuckv |
4724 |
tim |
1616 |
|
4725 |
|
|
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
4726 |
|
|
C-fortran interface functions. |
4727 |
|
|
|
4728 |
gezelter |
2199 |
2004-10-19 17:37 chuckv |
4729 |
tim |
1616 |
|
4730 |
|
|
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
4731 |
|
|
eam_module_inteface.h, gb_module_interface.h, |
4732 |
|
|
mpisimulation_module_interface.h, simulation_module_interface.h, |
4733 |
|
|
sticky_pair_module_interface.h: Added correct prototypes for |
4734 |
|
|
C-fortran interface functions. |
4735 |
|
|
|
4736 |
gezelter |
2199 |
2004-10-19 16:28 tim |
4737 |
tim |
1616 |
|
4738 |
|
|
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
4739 |
|
|
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
4740 |
|
|
test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
4741 |
|
|
test/math/RectMatrixTestCase.cpp, |
4742 |
|
|
test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
4743 |
|
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
4744 |
|
|
bugs get fixed at math library |
4745 |
|
|
|
4746 |
gezelter |
2199 |
2004-10-19 15:43 chuckv |
4747 |
tim |
1616 |
|
4748 |
|
|
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
4749 |
|
|
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
4750 |
|
|
DarkSide/mpisimulation_module_interface.h, |
4751 |
|
|
DarkSide/simulation_module_interface.h, |
4752 |
|
|
DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
4753 |
|
|
DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
4754 |
|
|
DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
4755 |
|
|
DarkSide/simulation_module.F90, do_Forces.F90, |
4756 |
|
|
fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
4757 |
|
|
notifycutoffs_module_interface.h: Added new files for fortran |
4758 |
|
|
interface. |
4759 |
|
|
|
4760 |
gezelter |
2199 |
2004-10-19 15:43 gezelter |
4761 |
tim |
1616 |
|
4762 |
|
|
* src/UseTheForce/Makefile: regressing |
4763 |
|
|
|
4764 |
gezelter |
2199 |
2004-10-19 15:40 gezelter |
4765 |
tim |
1616 |
|
4766 |
|
|
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
4767 |
|
|
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
4768 |
|
|
working on shapes for portability |
4769 |
|
|
|
4770 |
gezelter |
2199 |
2004-10-19 15:40 gezelter |
4771 |
tim |
1616 |
|
4772 |
|
|
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
4773 |
|
|
|
4774 |
gezelter |
2199 |
2004-10-19 13:21 chrisfen |
4775 |
tim |
1616 |
|
4776 |
|
|
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
4777 |
|
|
findBegin |
4778 |
|
|
|
4779 |
gezelter |
2199 |
2004-10-18 23:34 tim |
4780 |
tim |
1603 |
|
4781 |
|
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
4782 |
|
|
are fixed in Vector class |
4783 |
|
|
|
4784 |
gezelter |
2199 |
2004-10-18 23:28 tim |
4785 |
tim |
1603 |
|
4786 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
4787 |
|
|
some bugs in RectMatrixTestCase |
4788 |
|
|
|
4789 |
gezelter |
2199 |
2004-10-18 23:21 tim |
4790 |
tim |
1603 |
|
4791 |
|
|
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
4792 |
|
|
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
4793 |
|
|
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
4794 |
|
|
test/math/VectorTestCase.hpp: implement more test cases |
4795 |
|
|
|
4796 |
gezelter |
2199 |
2004-10-18 18:13 tim |
4797 |
tim |
1603 |
|
4798 |
|
|
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
4799 |
|
|
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
4800 |
|
|
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
4801 |
|
|
src/utils/StringTokenizer.hpp, test/math/Makefile, |
4802 |
|
|
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
4803 |
|
|
tests on math library |
4804 |
|
|
|
4805 |
gezelter |
2199 |
2004-10-18 16:03 tim |
4806 |
tim |
1603 |
|
4807 |
|
|
* test/math/: Makefile, QuaternionTestCase.cpp, |
4808 |
|
|
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
4809 |
|
|
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
4810 |
|
|
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
4811 |
|
|
more testing units |
4812 |
|
|
|
4813 |
gezelter |
2199 |
2004-10-18 12:07 tim |
4814 |
tim |
1603 |
|
4815 |
|
|
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
4816 |
|
|
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
4817 |
|
|
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
4818 |
|
|
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
4819 |
|
|
|
4820 |
gezelter |
2199 |
2004-10-18 11:30 gezelter |
4821 |
tim |
1603 |
|
4822 |
|
|
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
4823 |
|
|
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
4824 |
|
|
\phi) |
4825 |
|
|
|
4826 |
gezelter |
2199 |
2004-10-18 11:29 gezelter |
4827 |
tim |
1603 |
|
4828 |
|
|
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
4829 |
|
|
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
4830 |
|
|
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
4831 |
|
|
Shapes into OOPSE |
4832 |
|
|
|
4833 |
gezelter |
2199 |
2004-10-18 10:21 gezelter |
4834 |
tim |
1603 |
|
4835 |
|
|
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
4836 |
|
|
|
4837 |
gezelter |
2199 |
2004-10-18 00:23 tim |
4838 |
tim |
1603 |
|
4839 |
|
|
* test/math/VectorTestCase.hpp: adding vector test case |
4840 |
|
|
|
4841 |
gezelter |
2199 |
2004-10-18 00:23 tim |
4842 |
tim |
1603 |
|
4843 |
|
|
* src/utils/GenericFactory.hpp: adding generic factory and vector |
4844 |
|
|
test case |
4845 |
|
|
|
4846 |
gezelter |
2199 |
2004-10-16 20:19 tim |
4847 |
tim |
1594 |
|
4848 |
|
|
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
4849 |
|
|
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
4850 |
|
|
progress |
4851 |
|
|
|
4852 |
gezelter |
2199 |
2004-10-15 20:31 tim |
4853 |
tim |
1594 |
|
4854 |
|
|
* src/math/Quaternion.hpp: add quaternion class |
4855 |
|
|
|
4856 |
gezelter |
2199 |
2004-10-15 16:11 tim |
4857 |
tim |
1594 |
|
4858 |
|
|
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
4859 |
|
|
IfstrstreamTestCase.hpp: adding test file |
4860 |
|
|
|
4861 |
gezelter |
2199 |
2004-10-15 16:10 tim |
4862 |
tim |
1594 |
|
4863 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
4864 |
|
|
|
4865 |
gezelter |
2199 |
2004-10-15 15:42 tim |
4866 |
tim |
1594 |
|
4867 |
|
|
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
4868 |
|
|
|
4869 |
gezelter |
2199 |
2004-10-15 15:35 tim |
4870 |
tim |
1594 |
|
4871 |
|
|
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
4872 |
|
|
|
4873 |
gezelter |
2199 |
2004-10-15 15:34 tim |
4874 |
tim |
1594 |
|
4875 |
|
|
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
4876 |
|
|
namespace oopse |
4877 |
|
|
|
4878 |
gezelter |
2199 |
2004-10-15 14:38 chuckv |
4879 |
tim |
1594 |
|
4880 |
|
|
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
4881 |
|
|
XLF and XLC. |
4882 |
|
|
|
4883 |
gezelter |
2199 |
2004-10-15 13:28 tim |
4884 |
tim |
1594 |
|
4885 |
|
|
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
4886 |
|
|
adding ifstrstream test case |
4887 |
|
|
|
4888 |
gezelter |
2199 |
2004-10-15 13:20 tim |
4889 |
tim |
1594 |
|
4890 |
|
|
* src/io/basic_ifstrstream.hpp: fix include |
4891 |
|
|
|
4892 |
gezelter |
2199 |
2004-10-15 13:18 tim |
4893 |
tim |
1594 |
|
4894 |
|
|
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
4895 |
|
|
|
4896 |
gezelter |
2199 |
2004-10-15 13:17 tim |
4897 |
tim |
1594 |
|
4898 |
|
|
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
4899 |
|
|
|
4900 |
gezelter |
2199 |
2004-10-15 13:16 tim |
4901 |
tim |
1594 |
|
4902 |
|
|
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
4903 |
|
|
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
4904 |
|
|
|
4905 |
gezelter |
2199 |
2004-10-15 10:37 tim |
4906 |
tim |
1594 |
|
4907 |
|
|
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
4908 |
|
|
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
4909 |
|
|
|
4910 |
gezelter |
2199 |
2004-10-15 10:20 tim |
4911 |
tim |
1594 |
|
4912 |
|
|
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
4913 |
|
|
|
4914 |
gezelter |
2199 |
2004-10-15 10:19 tim |
4915 |
tim |
1594 |
|
4916 |
|
|
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
4917 |
|
|
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
4918 |
|
|
SquareMatrixTestCase class |
4919 |
|
|
|
4920 |
gezelter |
2199 |
2004-10-15 02:52 tim |
4921 |
tim |
1594 |
|
4922 |
|
|
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
4923 |
|
|
|
4924 |
gezelter |
2199 |
2004-10-14 18:28 tim |
4925 |
tim |
1594 |
|
4926 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
4927 |
|
|
Vector.hpp: math library in progress |
4928 |
|
|
|
4929 |
gezelter |
2199 |
2004-10-14 18:27 tim |
4930 |
tim |
1594 |
|
4931 |
|
|
* src/io/FileReader.hpp: FileReader in progress |
4932 |
|
|
|
4933 |
gezelter |
2199 |
2004-10-13 18:53 tim |
4934 |
tim |
1594 |
|
4935 |
|
|
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
4936 |
|
|
test in isOrthogonal of SquareMatrix is failed by some reasons |
4937 |
|
|
|
4938 |
gezelter |
2199 |
2004-10-13 17:28 tim |
4939 |
tim |
1594 |
|
4940 |
|
|
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
4941 |
|
|
class |
4942 |
|
|
|
4943 |
gezelter |
2199 |
2004-10-13 17:27 tim |
4944 |
tim |
1594 |
|
4945 |
|
|
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
4946 |
|
|
RectMatrixTestCase.hpp: adding testing unit |
4947 |
|
|
|
4948 |
gezelter |
2199 |
2004-10-13 17:24 tim |
4949 |
tim |
1594 |
|
4950 |
|
|
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
4951 |
|
|
|
4952 |
gezelter |
2199 |
2004-10-13 01:51 tim |
4953 |
tim |
1594 |
|
4954 |
|
|
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
4955 |
|
|
Vector3.hpp: refactory vector and matrix classes |
4956 |
|
|
|
4957 |
gezelter |
2199 |
2004-10-13 01:50 tim |
4958 |
tim |
1594 |
|
4959 |
|
|
* src/math/Vector3d.hpp: Remove some Makefile.in |
4960 |
|
|
|
4961 |
gezelter |
2199 |
2004-10-12 18:57 tim |
4962 |
tim |
1594 |
|
4963 |
|
|
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
4964 |
|
|
Matrix3x3d.hpp |
4965 |
|
|
|
4966 |
gezelter |
2199 |
2004-10-12 14:08 tim |
4967 |
tim |
1594 |
|
4968 |
|
|
* doc/: cppstyle.html, style.css: adding c++ coding style |
4969 |
|
|
|
4970 |
gezelter |
2199 |
2004-10-11 17:15 tim |
4971 |
tim |
1594 |
|
4972 |
|
|
* src/: constraints/AbstractClasses.hpp, |
4973 |
|
|
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
4974 |
|
|
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
4975 |
|
|
|
4976 |
gezelter |
2199 |
2004-10-11 16:54 tim |
4977 |
tim |
1594 |
|
4978 |
|
|
* scripts/filepp: fix a bug in filepp |
4979 |
|
|
|
4980 |
gezelter |
2199 |
2004-10-11 16:13 tim |
4981 |
tim |
1594 |
|
4982 |
|
|
* make/Makefile.in: using filepp to generate dependencies instead |
4983 |
|
|
of compilers |
4984 |
|
|
|
4985 |
gezelter |
2199 |
2004-10-11 16:10 tim |
4986 |
tim |
1594 |
|
4987 |
|
|
* scripts/filepp: filepp can be used to generate dependencies for |
4988 |
|
|
c/c++ now |
4989 |
|
|
|
4990 |
gezelter |
2199 |
2004-10-11 13:40 tim |
4991 |
tim |
1594 |
|
4992 |
|
|
* make/Makefile.in: remove -module from F90Options |
4993 |
|
|
|
4994 |
gezelter |
2199 |
2004-10-11 13:01 tim |
4995 |
tim |
1594 |
|
4996 |
|
|
* make/Makefile.in: adding rules to move fortran 90 module to |
4997 |
|
|
target directory |
4998 |
|
|
|
4999 |
gezelter |
2199 |
2004-10-11 10:43 gezelter |
5000 |
tim |
1594 |
|
5001 |
|
|
* make/Makefile.in: fixed makefile.in |
5002 |
|
|
|
5003 |
gezelter |
2199 |
2004-10-11 09:51 tim |
5004 |
tim |
1594 |
|
5005 |
|
|
* scripts/filepp: remove "use bytes" which causes problem in sgi |
5006 |
|
|
machine |
5007 |
|
|
|
5008 |
gezelter |
2199 |
2004-10-11 09:26 tim |
5009 |
tim |
1594 |
|
5010 |
|
|
* forceFields/Makefile: add Makefile |
5011 |
|
|
|
5012 |
gezelter |
2199 |
2004-10-11 09:23 tim |
5013 |
tim |
1594 |
|
5014 |
|
|
* samples/: water/dimer/Makefile, water/spce/Makefile, |
5015 |
|
|
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
5016 |
|
|
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
5017 |
|
|
directory |
5018 |
|
|
|
5019 |
gezelter |
2199 |
2004-10-11 09:23 tim |
5020 |
tim |
1594 |
|
5021 |
gezelter |
2199 |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
5022 |
|
|
Makefile |
5023 |
tim |
1594 |
|
5024 |
gezelter |
2199 |
2004-10-09 01:01 tim |
5025 |
tim |
1594 |
|
5026 |
gezelter |
2199 |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
5027 |
|
|
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
5028 |
|
|
Remove some Makefile.in |
5029 |
|
|
|
5030 |
|
|
2004-10-08 18:15 tim |
5031 |
|
|
|
5032 |
tim |
1594 |
* make/Makefile.in: [no log message] |
5033 |
|
|
|
5034 |
gezelter |
2199 |
2004-10-08 17:51 tim |
5035 |
tim |
1594 |
|
5036 |
|
|
* make/Makefile.in: fix make install |
5037 |
|
|
|
5038 |
gezelter |
2199 |
2004-10-08 17:10 tim |
5039 |
tim |
1594 |
|
5040 |
|
|
* make/Makefile.in: adding make install |
5041 |
|
|
|
5042 |
gezelter |
2199 |
2004-10-08 17:04 tim |
5043 |
tim |
1594 |
|
5044 |
gezelter |
2199 |
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
5045 |
|
|
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
5046 |
|
|
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
5047 |
tim |
1594 |
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
5048 |
|
|
water/ssde/Makefile, water/ssde/Makefile.in, |
5049 |
|
|
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
5050 |
|
|
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
5051 |
|
|
zcons/Makefile.in: add Makefile to sample directory |
5052 |
|
|
|
5053 |
gezelter |
2199 |
2004-10-06 18:03 gezelter |
5054 |
tim |
1594 |
|
5055 |
|
|
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
5056 |
|
|
stuff |
5057 |
|
|
|
5058 |
gezelter |
2199 |
2004-10-06 18:03 gezelter |
5059 |
tim |
1594 |
|
5060 |
|
|
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
5061 |
|
|
make/Doxyfile, src/applications/getopt.c, |
5062 |
|
|
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
5063 |
|
|
build fixes |
5064 |
|
|
|
5065 |
gezelter |
2199 |
2004-10-06 17:20 tim |
5066 |
tim |
1594 |
|
5067 |
|
|
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
5068 |
|
|
|
5069 |
gezelter |
2199 |
2004-10-06 17:19 tim |
5070 |
tim |
1594 |
|
5071 |
|
|
* scripts/filepp: filepp can handle different fortran module case |
5072 |
|
|
and suffix |
5073 |
|
|
|
5074 |
gezelter |
2199 |
2004-10-06 16:27 gezelter |
5075 |
tim |
1594 |
|
5076 |
|
|
* src/restraints/Restraints.cpp: Chris doesn't know about the |
5077 |
|
|
OOPSE-2.0 directory structure yet |
5078 |
|
|
|
5079 |
gezelter |
2199 |
2004-10-06 16:27 gezelter |
5080 |
tim |
1594 |
|
5081 |
|
|
* ChangeLog: Yeah yeah, we'lll get around to it later |
5082 |
|
|
|
5083 |
gezelter |
2199 |
2004-10-06 16:22 gezelter |
5084 |
gezelter |
1490 |
|
5085 |
tim |
1594 |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
5086 |
|
|
make/Makefile.in: cleaning up build process |
5087 |
gezelter |
1490 |
|
5088 |
gezelter |
2199 |
2004-10-06 15:01 chrisfen |
5089 |
tim |
1594 |
|
5090 |
|
|
* src/restraints/Restraints.cpp: made the file reading in |
5091 |
|
|
restraints more intelligent - no longer gives uninformative seg |
5092 |
|
|
faults |
5093 |
|
|
|
5094 |
gezelter |
2199 |
2004-10-06 14:55 gezelter |
5095 |
tim |
1594 |
|
5096 |
|
|
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
5097 |
|
|
|
5098 |
gezelter |
2199 |
2004-10-06 14:51 gezelter |
5099 |
gezelter |
1490 |
|
5100 |
tim |
1594 |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
5101 |
|
|
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
5102 |
gezelter |
1490 |
|
5103 |
gezelter |
2199 |
2004-10-06 13:53 tim |
5104 |
tim |
1594 |
|
5105 |
|
|
* make/: Makefile, Makefile.in: fix make statistics |
5106 |
|
|
|
5107 |
gezelter |
2199 |
2004-10-06 13:18 tim |
5108 |
tim |
1594 |
|
5109 |
|
|
* make/: Makefile, Makefile.in: adding GNU make functions to |
5110 |
|
|
combine all of the static libraries to a big library |
5111 |
|
|
|
5112 |
gezelter |
2199 |
2004-10-05 17:57 tim |
5113 |
tim |
1594 |
|
5114 |
|
|
* make/: Makefile, Makefile.in: adding shared library flag |
5115 |
|
|
|
5116 |
gezelter |
2199 |
2004-10-05 14:37 tim |
5117 |
tim |
1594 |
|
5118 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
5119 |
|
|
UseTheForce/mpiSimulation_module.F90, |
5120 |
|
|
UseTheForce/DarkSide/Makefile, |
5121 |
|
|
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
5122 |
|
|
mpiSimulation_module to DarkSide |
5123 |
|
|
|
5124 |
gezelter |
2199 |
2004-10-05 14:35 tim |
5125 |
tim |
1594 |
|
5126 |
|
|
* make/: Makefile, Makefile.in: building MPI version;using static |
5127 |
|
|
library instead of shared library |
5128 |
|
|
|
5129 |
gezelter |
2199 |
2004-10-05 09:14 tim |
5130 |
tim |
1594 |
|
5131 |
|
|
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
5132 |
|
|
to filepp |
5133 |
|
|
|
5134 |
gezelter |
2199 |
2004-10-04 15:56 tim |
5135 |
tim |
1594 |
|
5136 |
|
|
* make/: Makefile, Makefile.in: add make cvslog |
5137 |
|
|
|
5138 |
gezelter |
2199 |
2004-10-04 11:24 gezelter |
5139 |
tim |
1594 |
|
5140 |
|
|
* make/: Makefile, Makefile.in: more work on the parallel build |
5141 |
|
|
|
5142 |
gezelter |
2199 |
2004-10-04 11:06 gezelter |
5143 |
tim |
1594 |
|
5144 |
|
|
* make/: Makefile, Makefile.in: changes to backport declare flags |
5145 |
|
|
|
5146 |
gezelter |
2199 |
2004-10-04 10:27 gezelter |
5147 |
tim |
1594 |
|
5148 |
|
|
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
5149 |
|
|
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
5150 |
|
|
shapes |
5151 |
|
|
|
5152 |
gezelter |
2199 |
2004-10-01 23:40 tim |
5153 |
tim |
1594 |
|
5154 |
|
|
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
5155 |
|
|
|
5156 |
gezelter |
2199 |
2004-10-01 23:22 tim |
5157 |
tim |
1594 |
|
5158 |
|
|
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
5159 |
|
|
|
5160 |
gezelter |
2199 |
2004-10-01 16:59 tim |
5161 |
tim |
1594 |
|
5162 |
|
|
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
5163 |
|
|
|
5164 |
gezelter |
2199 |
2004-10-01 16:22 gezelter |
5165 |
gezelter |
1490 |
|
5166 |
tim |
1594 |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
5167 |
|
|
few minor build changes |
5168 |
gezelter |
1490 |
|
5169 |
gezelter |
2199 |
2004-10-01 16:11 tim |
5170 |
tim |
1594 |
|
5171 |
|
|
* scripts/filepp: adding fortran90 make dependency tool |
5172 |
|
|
|
5173 |
gezelter |
2199 |
2004-09-30 10:41 tim |
5174 |
tim |
1594 |
|
5175 |
|
|
* make/: Makefile, Makefile.in: make clean is smart enough to only |
5176 |
|
|
remove object files belong to current package. turn off silent |
5177 |
|
|
mode |
5178 |
|
|
|
5179 |
gezelter |
2199 |
2004-09-29 16:55 tim |
5180 |
tim |
1594 |
|
5181 |
|
|
* src/: Makefile, UseTheForce/Makefile, |
5182 |
|
|
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
5183 |
|
|
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
5184 |
|
|
brains/Makedepend, brains/Makefile, constraints/Makefile, |
5185 |
|
|
integrators/Makefile, io/Makefile, math/Makefile, |
5186 |
|
|
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
5187 |
|
|
restraints/Makefile, types/Makefile, utils/Makefile, |
5188 |
|
|
visitors/Makefile: define DEV_ROOT as relative path |
5189 |
|
|
|
5190 |
gezelter |
2199 |
2004-09-29 16:54 tim |
5191 |
tim |
1594 |
|
5192 |
|
|
* make/: Makefile, Makefile.in: get the relative path by shell |
5193 |
|
|
script |
5194 |
|
|
|
5195 |
gezelter |
2199 |
2004-09-29 16:32 tim |
5196 |
tim |
1594 |
|
5197 |
|
|
* make/Makefile: eliminate DEV_ROOT by relative path |
5198 |
|
|
|
5199 |
gezelter |
2199 |
2004-09-29 13:37 tim |
5200 |
tim |
1594 |
|
5201 |
|
|
* make/Makefile.in: add PackageLibs; fix dependency rule |
5202 |
|
|
|
5203 |
gezelter |
2199 |
2004-09-29 12:57 gezelter |
5204 |
gezelter |
1490 |
|
5205 |
gezelter |
1536 |
* configure, ac-tools/configure.in: updates |
5206 |
gezelter |
1490 |
|
5207 |
gezelter |
2199 |
2004-09-29 12:56 gezelter |
5208 |
tim |
1594 |
|
5209 |
gezelter |
2199 |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
5210 |
tim |
1594 |
|
5211 |
gezelter |
2199 |
2004-09-29 12:46 tim |
5212 |
gezelter |
1490 |
|
5213 |
gezelter |
1536 |
* Makefile: If makefile does not exist, print error message |
5214 |
gezelter |
1490 |
|
5215 |
gezelter |
2199 |
2004-09-29 12:12 tim |
5216 |
tim |
1594 |
|
5217 |
|
|
* make/: Make.conf.in, Makefile: fix dependencies rule |
5218 |
|
|
|
5219 |
gezelter |
2199 |
2004-09-29 10:58 gezelter |
5220 |
gezelter |
1490 |
|
5221 |
tim |
1594 |
* Makefile, make/Makefile: still working on build process |
5222 |
gezelter |
1490 |
|
5223 |
gezelter |
2199 |
2004-09-29 10:00 tim |
5224 |
tim |
1594 |
|
5225 |
|
|
* make/Makefile: add print statment to rules |
5226 |
|
|
|
5227 |
gezelter |
2199 |
2004-09-29 09:59 tim |
5228 |
tim |
1594 |
|
5229 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
5230 |
|
|
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
5231 |
|
|
applications/simpleBuilder/Makefile, brains/Makefile, |
5232 |
|
|
constraints/Makefile, integrators/Makefile, io/Makefile, |
5233 |
|
|
math/Makefile, minimizers/Makefile, primitives/Makefile, |
5234 |
|
|
profiling/Makefile, restraints/Makefile, types/Makefile, |
5235 |
|
|
utils/Makefile, visitors/Makefile: change Makefile to relative path |
5236 |
|
|
|
5237 |
gezelter |
2199 |
2004-09-28 21:55 tim |
5238 |
tim |
1594 |
|
5239 |
|
|
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
5240 |
|
|
which cause headache in bulding libutils |
5241 |
|
|
|
5242 |
gezelter |
2199 |
2004-09-28 18:24 tim |
5243 |
tim |
1594 |
|
5244 |
|
|
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
5245 |
|
|
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
5246 |
|
|
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
5247 |
|
|
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
5248 |
|
|
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
5249 |
|
|
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
5250 |
|
|
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
5251 |
|
|
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
5252 |
|
|
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
5253 |
|
|
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
5254 |
|
|
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
5255 |
|
|
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
5256 |
|
|
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
5257 |
|
|
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
5258 |
|
|
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
5259 |
|
|
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
5260 |
|
|
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
5261 |
|
|
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
5262 |
|
|
change directory structure of application. Every executable file is |
5263 |
|
|
replaced in seperate directory |
5264 |
|
|
|
5265 |
gezelter |
2199 |
2004-09-28 17:15 gezelter |
5266 |
tim |
1594 |
|
5267 |
|
|
* lib/dummy: Keep that lib around, please. |
5268 |
|
|
|
5269 |
gezelter |
2199 |
2004-09-28 17:14 gezelter |
5270 |
gezelter |
1490 |
|
5271 |
tim |
1594 |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
5272 |
|
|
starting a configure version |
5273 |
gezelter |
1490 |
|
5274 |
gezelter |
2199 |
2004-09-28 16:08 tim |
5275 |
tim |
1594 |
|
5276 |
|
|
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
5277 |
|
|
UseTheForce/DarkSide/Makefile, |
5278 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
5279 |
|
|
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
5280 |
|
|
brains/Makefile, brains/simulation_module.F90: move fortran files |
5281 |
|
|
around to solve dependency problem |
5282 |
|
|
|
5283 |
gezelter |
2199 |
2004-09-28 15:43 tim |
5284 |
gezelter |
1490 |
|
5285 |
tim |
1594 |
* Makefile, src/UseTheForce/ForceFields.hpp, |
5286 |
|
|
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
5287 |
|
|
src/applications/Makedepend, src/applications/Makefile, |
5288 |
|
|
src/brains/Makedepend, src/brains/simulation_module.F90, |
5289 |
|
|
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
5290 |
|
|
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
5291 |
|
|
src/utils/Makefile: [no log message] |
5292 |
gezelter |
1490 |
|
5293 |
gezelter |
2199 |
2004-09-28 15:41 tim |
5294 |
tim |
1594 |
|
5295 |
|
|
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
5296 |
|
|
problem |
5297 |
|
|
|
5298 |
gezelter |
2199 |
2004-09-28 11:13 tim |
5299 |
tim |
1594 |
|
5300 |
|
|
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
5301 |
|
|
src/io/Makefile: add yacc and lex rules |
5302 |
|
|
|
5303 |
gezelter |
2199 |
2004-09-27 15:24 tim |
5304 |
tim |
1594 |
|
5305 |
|
|
* make/Makefile: adding include path to F90Options |
5306 |
|
|
|
5307 |
gezelter |
2199 |
2004-09-27 15:13 tim |
5308 |
tim |
1594 |
|
5309 |
|
|
* make/Makefile: change suffix from .cc to .cpp |
5310 |
|
|
|
5311 |
gezelter |
2199 |
2004-09-24 11:27 tim |
5312 |
tim |
1594 |
|
5313 |
|
|
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
5314 |
|
|
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
5315 |
|
|
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
5316 |
|
|
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
5317 |
|
|
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
5318 |
|
|
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
5319 |
|
|
UseTheForce/DarkSide/calc_LJ_FF.F90, |
5320 |
|
|
UseTheForce/DarkSide/notifyCutoffs.F90, |
5321 |
|
|
UseTheForce/DarkSide/switch_module.F90, |
5322 |
|
|
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
5323 |
|
|
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
5324 |
|
|
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
5325 |
|
|
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
5326 |
|
|
applications/MoLocator.cpp, applications/MoLocator.hpp, |
5327 |
|
|
applications/cmdline.c, applications/nanoBuilder.cpp, |
5328 |
|
|
applications/oopse.cpp, applications/simpleBuilder.cpp, |
5329 |
|
|
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
5330 |
|
|
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
5331 |
|
|
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
5332 |
|
|
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
5333 |
|
|
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
5334 |
|
|
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
5335 |
|
|
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
5336 |
|
|
integrators/Integrator.hpp, integrators/NPT.cpp, |
5337 |
|
|
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
5338 |
|
|
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
5339 |
|
|
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
5340 |
|
|
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
5341 |
|
|
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
5342 |
|
|
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
5343 |
|
|
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
5344 |
|
|
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
5345 |
|
|
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
5346 |
|
|
math/MatVec3.h, math/randomSPRNG.cpp, |
5347 |
|
|
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
5348 |
|
|
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
5349 |
|
|
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
5350 |
|
|
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
5351 |
|
|
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
5352 |
|
|
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
5353 |
|
|
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
5354 |
|
|
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
5355 |
|
|
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
5356 |
|
|
primitives/RigidBody.hpp, primitives/SRI.hpp, |
5357 |
|
|
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
5358 |
|
|
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
5359 |
|
|
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
5360 |
|
|
restraints/Restraints.hpp, types/AtomStamp.cpp, |
5361 |
|
|
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
5362 |
|
|
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
5363 |
|
|
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
5364 |
|
|
types/MakeStamps.cpp, types/MakeStamps.hpp, |
5365 |
|
|
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
5366 |
|
|
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
5367 |
|
|
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
5368 |
|
|
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
5369 |
|
|
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
5370 |
|
|
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
5371 |
|
|
utils/simError.c, visitors/AtomVisitor.cpp, |
5372 |
|
|
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
5373 |
|
|
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
5374 |
|
|
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
5375 |
|
|
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
5376 |
|
|
visitors/ZconsVisitor.hpp: change the #include in source files |
5377 |
|
|
|
5378 |
gezelter |
2199 |
2004-09-23 23:16 gezelter |
5379 |
gezelter |
1490 |
|
5380 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
5381 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
5382 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
5383 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
5384 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
5385 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
5386 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
5387 |
|
|
src/UseTheForce/fForceField.h, |
5388 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
5389 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
5390 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
5391 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
5392 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
5393 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
5394 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
5395 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
5396 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
5397 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
5398 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
5399 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
5400 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
5401 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
5402 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
5403 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
5404 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
5405 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
5406 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
5407 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
5408 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
5409 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
5410 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
5411 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
5412 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
5413 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
5414 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
5415 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
5416 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
5417 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
5418 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
5419 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
5420 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
5421 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
5422 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
5423 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
5424 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
5425 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
5426 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
5427 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
5428 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
5429 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
5430 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
5431 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
5432 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
5433 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
5434 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
5435 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
5436 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
5437 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
5438 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
5439 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
5440 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
5441 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
5442 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
5443 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
5444 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
5445 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
5446 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
5447 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
5448 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
5449 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
5450 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
5451 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
5452 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
5453 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
5454 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
5455 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
5456 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
5457 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
5458 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
5459 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
5460 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
5461 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
5462 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
5463 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
5464 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
5465 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
5466 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
5467 |
|
|
src/utils/simError.c, src/utils/simError.h, |
5468 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
5469 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
5470 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
5471 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
5472 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
5473 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
5474 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
5475 |
gezelter |
2199 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
5476 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
5477 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
5478 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
5479 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
5480 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
5481 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
5482 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
5483 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
5484 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
5485 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
5486 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
5487 |
|
|
src/applications/LatticeCreator.cpp, |
5488 |
|
|
src/applications/LatticeCreator.hpp, |
5489 |
|
|
src/applications/LatticeFactory.cpp, |
5490 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
5491 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
5492 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
5493 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
5494 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
5495 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
5496 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
5497 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
5498 |
|
|
src/applications/simpleBuilder.ggo, |
5499 |
|
|
src/applications/simpleBuilderCmd.c, |
5500 |
|
|
src/integrators/AbstractClasses.hpp, |
5501 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
5502 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
5503 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
5504 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
5505 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
5506 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
5507 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
5508 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
5509 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
5510 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
5511 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
5512 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
5513 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
5514 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
5515 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
5516 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
5517 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
5518 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
5519 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
5520 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
5521 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
5522 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
5523 |
gezelter |
2199 |
samples/argon/500.in, samples/argon/500.md, |
5524 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
5525 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
5526 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
5527 |
tim |
1594 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
5528 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
5529 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
5530 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
5531 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
5532 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
5533 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
5534 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
5535 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
5536 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
5537 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
5538 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
5539 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
5540 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
5541 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
5542 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
5543 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
5544 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
5545 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
5546 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
5547 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
5548 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
5549 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
5550 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
5551 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
5552 |
gezelter |
1490 |
|
5553 |
gezelter |
2199 |
2004-09-23 23:16 gezelter |
5554 |
gezelter |
1490 |
|
5555 |
gezelter |
1536 |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
5556 |
tim |
1594 |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
5557 |
|
|
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
5558 |
|
|
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
5559 |
|
|
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
5560 |
|
|
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
5561 |
|
|
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
5562 |
|
|
src/UseTheForce/fForceField.h, |
5563 |
|
|
src/UseTheForce/fSwitchingFunction.h, |
5564 |
|
|
src/UseTheForce/fortranWrapDefines.hpp, |
5565 |
|
|
src/UseTheForce/fortranWrappers.cpp, |
5566 |
|
|
src/UseTheForce/fortranWrappers.hpp, |
5567 |
|
|
src/UseTheForce/mpiComponentPlan.h, |
5568 |
|
|
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
5569 |
|
|
src/UseTheForce/mpiSimulation_module.F90, |
5570 |
|
|
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
5571 |
|
|
src/UseTheForce/DarkSide/atype_module.F90, |
5572 |
|
|
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
5573 |
|
|
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
5574 |
|
|
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
5575 |
|
|
src/UseTheForce/DarkSide/calc_eam.F90, |
5576 |
|
|
src/UseTheForce/DarkSide/calc_gb.F90, |
5577 |
|
|
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
5578 |
|
|
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
5579 |
|
|
src/UseTheForce/DarkSide/force_globals.F90, |
5580 |
|
|
src/UseTheForce/DarkSide/neighborLists.F90, |
5581 |
|
|
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
5582 |
|
|
src/UseTheForce/DarkSide/switch_module.F90, |
5583 |
|
|
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
5584 |
|
|
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
5585 |
|
|
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
5586 |
|
|
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
5587 |
|
|
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
5588 |
|
|
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
5589 |
|
|
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
5590 |
|
|
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
5591 |
|
|
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
5592 |
|
|
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
5593 |
|
|
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
5594 |
|
|
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
5595 |
|
|
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
5596 |
|
|
src/types/BondStamp.hpp, src/types/Component.cpp, |
5597 |
|
|
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
5598 |
|
|
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
5599 |
|
|
src/types/MakeStamps.hpp, src/types/Makefile, |
5600 |
|
|
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
5601 |
|
|
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
5602 |
|
|
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
5603 |
|
|
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
5604 |
|
|
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
5605 |
|
|
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
5606 |
|
|
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
5607 |
|
|
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
5608 |
|
|
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
5609 |
|
|
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
5610 |
|
|
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
5611 |
|
|
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
5612 |
|
|
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
5613 |
|
|
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
5614 |
|
|
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
5615 |
|
|
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
5616 |
|
|
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
5617 |
|
|
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
5618 |
|
|
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
5619 |
|
|
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
5620 |
|
|
src/minimizers/OOPSEMinimizer.cpp, |
5621 |
|
|
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
5622 |
|
|
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
5623 |
|
|
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
5624 |
|
|
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
5625 |
|
|
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
5626 |
|
|
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
5627 |
|
|
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
5628 |
|
|
src/primitives/Makefile, src/primitives/Molecule.cpp, |
5629 |
|
|
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
5630 |
|
|
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
5631 |
|
|
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
5632 |
|
|
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
5633 |
|
|
src/restraints/Makefile, src/restraints/Restraints.cpp, |
5634 |
|
|
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
5635 |
|
|
src/utils/GenericData.hpp, src/utils/Makefile, |
5636 |
|
|
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
5637 |
|
|
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
5638 |
|
|
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
5639 |
|
|
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
5640 |
|
|
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
5641 |
|
|
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
5642 |
|
|
src/utils/simError.c, src/utils/simError.h, |
5643 |
|
|
src/utils/status_module.F90, src/utils/vector_class.F90, |
5644 |
|
|
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
5645 |
|
|
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
5646 |
|
|
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
5647 |
|
|
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
5648 |
|
|
src/visitors/RigidBodyVisitor.cpp, |
5649 |
|
|
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
5650 |
gezelter |
2199 |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
5651 |
tim |
1594 |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
5652 |
|
|
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
5653 |
|
|
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
5654 |
|
|
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
5655 |
|
|
samples/zcons/Makefile.in, samples/zcons/water.md, |
5656 |
|
|
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
5657 |
|
|
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
5658 |
|
|
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
5659 |
|
|
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
5660 |
|
|
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
5661 |
|
|
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
5662 |
|
|
src/applications/LatticeCreator.cpp, |
5663 |
|
|
src/applications/LatticeCreator.hpp, |
5664 |
|
|
src/applications/LatticeFactory.cpp, |
5665 |
|
|
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
5666 |
|
|
src/applications/Makefile, src/applications/MoLocator.cpp, |
5667 |
|
|
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
5668 |
|
|
src/applications/cmdline.c, src/applications/cmdline.h, |
5669 |
|
|
src/applications/getopt.c, src/applications/getopt1.c, |
5670 |
|
|
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
5671 |
|
|
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
5672 |
|
|
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
5673 |
|
|
src/applications/simpleBuilder.ggo, |
5674 |
|
|
src/applications/simpleBuilderCmd.c, |
5675 |
|
|
src/integrators/AbstractClasses.hpp, |
5676 |
|
|
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
5677 |
|
|
src/integrators/Integrator.hpp, src/integrators/Makefile, |
5678 |
|
|
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
5679 |
|
|
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
5680 |
|
|
src/integrators/NVT.cpp, src/profiling/Makefile, |
5681 |
|
|
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
5682 |
|
|
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
5683 |
|
|
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
5684 |
|
|
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
5685 |
|
|
samples/water/dimer/two.in, samples/water/dimer/two.md, |
5686 |
|
|
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
5687 |
|
|
samples/water/spce/spce.in, samples/water/spce/spce.md, |
5688 |
|
|
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
5689 |
|
|
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
5690 |
|
|
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
5691 |
|
|
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
5692 |
|
|
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
5693 |
|
|
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
5694 |
|
|
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
5695 |
|
|
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
5696 |
|
|
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
5697 |
|
|
samples/alkane/butane.in, samples/alkane/butane.md, |
5698 |
gezelter |
2199 |
samples/argon/500.in, samples/argon/500.md, |
5699 |
|
|
samples/argon/Makefile.in, samples/argon/ar864.in, |
5700 |
|
|
samples/argon/ar864.md, samples/argon/argonNVT.in, |
5701 |
|
|
samples/argon/argonNVT.md, samples/argon/lj.md, |
5702 |
tim |
1594 |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
5703 |
|
|
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
5704 |
|
|
samples/lipid/water.md, samples/minimizer/Makefile.in, |
5705 |
|
|
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
5706 |
|
|
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
5707 |
|
|
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
5708 |
|
|
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
5709 |
|
|
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
5710 |
|
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
5711 |
|
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
5712 |
|
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
5713 |
|
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
5714 |
|
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
5715 |
|
|
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
5716 |
|
|
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
5717 |
|
|
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
5718 |
|
|
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
5719 |
|
|
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
5720 |
gezelter |
1536 |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
5721 |
|
|
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
5722 |
tim |
1594 |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
5723 |
|
|
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
5724 |
|
|
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
5725 |
|
|
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
5726 |
tim |
1648 |
forceFields/Pt.VC.funcfl: Initial revision |
5727 |
gezelter |
1490 |
|