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Comparing trunk/OOPSE-4/ChangeLog (file contents):
Revision 2761 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 2762 by chrisfen, Fri May 19 21:26:41 2006 UTC

# Line 1 | Line 1
1 < 2006-05-17 14:54  gezelter
1 > 2006-05-19 16:45  tim
2  
3 +        * src/io/DumpWriter.cpp: Fix a bug of printing empty line in
4 +        DumpWriter
5 +
6 + 2006-05-19 11:11  tim
7 +
8 +        * make/Makefile.in: change the order of include path and library
9 +        path
10 +
11 + 2006-05-17 17:51  tim
12 +
13 +        * ChangeLog, samples/water/ssd/ssd.md, src/config.h.in,
14 +        src/UseTheForce/EAM_FF.cpp, src/UseTheForce/EAM_FF.hpp,
15 +        src/UseTheForce/ForceField.cpp, src/UseTheForce/ForceField.hpp,
16 +        src/UseTheForce/SHAPES_FF.cpp, src/UseTheForce/SHAPES_FF.hpp,
17 +        src/UseTheForce/doForces_interface.h,
18 +        src/UseTheForce/fForceOptions.h,
19 +        src/UseTheForce/DarkSide/eam_interface.h,
20 +        src/UseTheForce/DarkSide/electrostatic_interface.h,
21 +        src/UseTheForce/DarkSide/gb_interface.h,
22 +        src/UseTheForce/DarkSide/lj_interface.h,
23 +        src/UseTheForce/DarkSide/shapes_interface.h,
24 +        src/UseTheForce/DarkSide/simulation_interface.h,
25 +        src/UseTheForce/DarkSide/sticky_interface.h,
26 +        src/UseTheForce/DarkSide/suttonchen_interface.h,
27 +        src/applications/dynamicProps/CrossTimeCorrFunc.cpp,
28 +        src/applications/dynamicProps/CrossTimeCorrFunc.hpp,
29 +        src/applications/dynamicProps/DipoleCorrFunc.cpp,
30 +        src/applications/dynamicProps/DipoleCorrFunc.hpp,
31 +        src/applications/dynamicProps/LegendreCorrFunc.cpp,
32 +        src/applications/dynamicProps/LegendreCorrFunc.hpp,
33 +        src/applications/dynamicProps/ParticleTimeCorrFunc.cpp,
34 +        src/applications/dynamicProps/ParticleTimeCorrFunc.hpp,
35 +        src/applications/dynamicProps/RCorrFunc.cpp,
36 +        src/applications/dynamicProps/RCorrFunc.hpp,
37 +        src/applications/dynamicProps/TimeCorrFunc.hpp,
38 +        src/applications/dynamicProps/VCorrFunc.cpp,
39 +        src/applications/dynamicProps/VCorrFunc.hpp,
40 +        src/applications/hydrodynamics/Makefile,
41 +        src/applications/nanoRodBuilder/GeometryBuilder.cpp,
42 +        src/applications/nanoRodBuilder/GeometryBuilder.hpp,
43 +        src/applications/nanoRodBuilder/nanorodBuilder.cpp,
44 +        src/applications/randomBuilder/randomBuilder.cpp,
45 +        src/applications/simpleBuilder/randomBuilder.cpp,
46 +        src/applications/staticProps/DensityPlot.cpp,
47 +        src/applications/staticProps/DensityPlot.hpp,
48 +        src/applications/staticProps/GofAngle2.cpp,
49 +        src/applications/staticProps/GofAngle2.hpp,
50 +        src/applications/staticProps/GofR.cpp,
51 +        src/applications/staticProps/GofR.hpp,
52 +        src/applications/staticProps/GofRAngle.cpp,
53 +        src/applications/staticProps/GofRAngle.hpp,
54 +        src/applications/staticProps/GofXyz.cpp,
55 +        src/applications/staticProps/GofXyz.hpp,
56 +        src/applications/staticProps/Hxy.cpp,
57 +        src/applications/staticProps/Hxy.hpp,
58 +        src/applications/staticProps/P2OrderParameter.cpp,
59 +        src/applications/staticProps/P2OrderParameter.hpp,
60 +        src/applications/staticProps/RhoZ.cpp,
61 +        src/applications/staticProps/RhoZ.hpp,
62 +        src/applications/staticProps/SCDOrderParameter.cpp,
63 +        src/applications/staticProps/SCDOrderParameter.hpp,
64 +        src/applications/staticProps/StaticProps.cpp,
65 +        src/brains/BlockSnapshotManager.cpp, src/brains/DataStorage.cpp,
66 +        src/brains/DataStorage.hpp, src/brains/ForceManager.cpp,
67 +        src/brains/SimCreator.cpp, src/brains/SimInfo.cpp,
68 +        src/brains/SimInfo.hpp, src/brains/Snapshot.cpp,
69 +        src/brains/Snapshot.hpp, src/brains/Stats.hpp,
70 +        src/brains/Thermo.cpp, src/brains/Thermo.hpp,
71 +        src/brains/fSimulation.h, src/constraints/ConstraintElem.hpp,
72 +        src/constraints/ConstraintPair.hpp, src/constraints/Rattle.cpp,
73 +        src/constraints/Rattle.hpp, src/constraints/ZconsStruct.hpp,
74 +        src/constraints/ZconstraintForceManager.cpp,
75 +        src/constraints/ZconstraintForceManager.hpp,
76 +        src/hydrodynamics/Ellipsoid.cpp, src/hydrodynamics/Ellipsoid.hpp,
77 +        src/hydrodynamics/Shape.hpp, src/hydrodynamics/Sphere.cpp,
78 +        src/hydrodynamics/Sphere.hpp, src/integrators/DLM.cpp,
79 +        src/integrators/DLM.hpp, src/integrators/Integrator.hpp,
80 +        src/integrators/LDForceManager.cpp,
81 +        src/integrators/LDForceManager.hpp,
82 +        src/integrators/LangevinDynamics.cpp,
83 +        src/integrators/LangevinDynamics.hpp, src/integrators/NPAT.cpp,
84 +        src/integrators/NPAT.hpp, src/integrators/NPT.cpp,
85 +        src/integrators/NPT.hpp, src/integrators/NPTf.cpp,
86 +        src/integrators/NPTf.hpp, src/integrators/NPTi.cpp,
87 +        src/integrators/NPTi.hpp, src/integrators/NPTxyz.cpp,
88 +        src/integrators/NPTxyz.hpp, src/integrators/NPrT.cpp,
89 +        src/integrators/NPrT.hpp, src/integrators/NVE.cpp,
90 +        src/integrators/NVE.hpp, src/integrators/NVT.cpp,
91 +        src/integrators/NVT.hpp, src/integrators/RotationAlgorithm.hpp,
92 +        src/integrators/Velocitizer.cpp, src/integrators/Velocitizer.hpp,
93 +        src/integrators/VelocityVerletIntegrator.cpp,
94 +        src/integrators/VelocityVerletIntegrator.hpp,
95 +        src/io/AtomTypesSectionParser.cpp,
96 +        src/io/BendTypesSectionParser.cpp,
97 +        src/io/BondTypesSectionParser.cpp,
98 +        src/io/ChargeAtomTypesSectionParser.cpp,
99 +        src/io/DirectionalAtomTypesSectionParser.cpp,
100 +        src/io/DumpReader.cpp, src/io/DumpWriter.cpp,
101 +        src/io/EAMAtomTypesSectionParser.cpp,
102 +        src/io/EAMAtomTypesSectionParser.hpp, src/io/ForceFieldOptions.hpp,
103 +        src/io/Globals.hpp, src/io/MultipoleAtomTypesSectionParser.cpp,
104 +        src/io/RestReader.cpp, src/io/RestReader.hpp,
105 +        src/io/RestWriter.cpp, src/io/TorsionTypesSectionParser.cpp,
106 +        src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp,
107 +        src/lattice/CubicLattice.cpp, src/lattice/CubicLattice.hpp,
108 +        src/lattice/FCCLattice.cpp, src/lattice/Lattice.cpp,
109 +        src/lattice/Lattice.hpp, src/lattice/shapedLattice.cpp,
110 +        src/lattice/shapedLattice.hpp, src/math/ChebyshevPolynomials.hpp,
111 +        src/math/CholeskyDecomposition.hpp,
112 +        src/math/LegendrePolynomial.cpp, src/math/LegendrePolynomial.hpp,
113 +        src/math/MatVec3.c, src/math/MatVec3.h,
114 +        src/math/MersenneTwister.hpp, src/math/Polynomial.hpp,
115 +        src/math/Quaternion.hpp, src/math/RandNumGen.hpp,
116 +        src/math/RealSphericalHarmonic.cpp,
117 +        src/math/RealSphericalHarmonic.hpp, src/math/SquareMatrix.hpp,
118 +        src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
119 +        src/math/Vector3.hpp, src/mdParser/MDTreeParser.cpp,
120 +        src/mdParser/MDTreeParser.g, src/mdParser/MDTreeParser.hpp,
121 +        src/minimizers/CGFamilyMinimizer.cpp,
122 +        src/minimizers/CGFamilyMinimizer.hpp, src/minimizers/Minimizer.cpp,
123 +        src/minimizers/Minimizer.hpp,
124 +        src/minimizers/MinimizerParameterSet.hpp, src/minimizers/PRCG.cpp,
125 +        src/minimizers/SDMinimizer.cpp, src/minimizers/SDMinimizer.hpp,
126 +        src/primitives/Atom.cpp, src/primitives/Atom.hpp,
127 +        src/primitives/Bend.cpp, src/primitives/Bend.hpp,
128 +        src/primitives/Bond.hpp, src/primitives/CutoffGroup.hpp,
129 +        src/primitives/DirectionalAtom.cpp,
130 +        src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp,
131 +        src/primitives/GhostBend.hpp, src/primitives/GhostTorsion.cpp,
132 +        src/primitives/GhostTorsion.hpp, src/primitives/Molecule.cpp,
133 +        src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp,
134 +        src/primitives/RigidBody.hpp, src/primitives/StuntDouble.hpp,
135 +        src/primitives/Torsion.cpp, src/primitives/Torsion.hpp,
136 +        src/primitives/UreyBradleyBend.cpp,
137 +        src/primitives/UreyBradleyBend.hpp, src/profiling/mdProfile.cpp,
138 +        src/restraints/Restraints.cpp, src/restraints/Restraints.hpp,
139 +        src/restraints/ThermoIntegrationForceManager.hpp,
140 +        src/selection/DistanceFinder.cpp, src/selection/DistanceFinder.hpp,
141 +        src/selection/SelectionEvaluator.cpp,
142 +        src/selection/SelectionEvaluator.hpp, src/types/AtomStamp.cpp,
143 +        src/types/AtomStamp.hpp, src/types/AtomType.cpp,
144 +        src/types/AtomType.hpp, src/types/AtomTypeProperties.h,
145 +        src/types/BendType.hpp, src/types/BondType.hpp,
146 +        src/types/CharmmTorsionType.hpp, src/types/CubicBendType.hpp,
147 +        src/types/CubicBondType.hpp, src/types/CubicTorsionType.hpp,
148 +        src/types/DirectionalAtomType.cpp,
149 +        src/types/DirectionalAtomType.hpp, src/types/FixedBondType.hpp,
150 +        src/types/HarmonicBendType.hpp, src/types/HarmonicBondType.hpp,
151 +        src/types/MorseBondType.hpp, src/types/OplsTorsionType.hpp,
152 +        src/types/PolynomialBendType.hpp, src/types/PolynomialBondType.hpp,
153 +        src/types/PolynomialTorsionType.hpp, src/types/QuarticBendType.hpp,
154 +        src/types/QuarticBondType.hpp, src/types/QuarticTorsionType.hpp,
155 +        src/types/ShapeAtomType.cpp, src/types/ShapeAtomType.hpp,
156 +        src/types/TorsionType.hpp, src/types/UreyBradleyBendType.hpp,
157 +        src/types/ZconsStamp.hpp, src/utils/Algorithm.hpp,
158 +        src/utils/GenericData.hpp, src/utils/MoLocator.cpp,
159 +        src/utils/MoLocator.hpp, src/utils/NumericConstant.hpp,
160 +        src/utils/OOPSEConstant.hpp, src/utils/ParameterManager.hpp,
161 +        src/utils/StringTokenizer.cpp, src/utils/StringTokenizer.hpp,
162 +        src/utils/Utility.hpp, src/utils/physmem.c, src/utils/physmem.h,
163 +        src/utils/residentMem.c, src/utils/residentMem.h,
164 +        src/visitors/ZconsVisitor.cpp, src/visitors/ZconsVisitor.hpp:
165 +        Adding single precision capabilities to c++ side
166 +
167 + 2006-05-17 15:54  gezelter
168 +
169          * configure, ac-tools/configure.in, make/Makefile.in,
170          src/UseTheForce/doForces.F90,
171          src/UseTheForce/DarkSide/neighborLists.F90,
# Line 9 | Line 175
175          src/utils/definitions.F90: Adding single precision capabilities to
176          the fortran side
177  
178 < 2006-05-17 11:10  gezelter
178 > 2006-05-17 12:10  gezelter
179  
180          * configure, ac-tools/configure.in, src/config.h.in: adding
181          --enable-single to configure script
182  
183 < 2006-05-17 10:37  gezelter
183 > 2006-05-17 11:37  gezelter
184  
185          * ac-tools/aclocal.m4, src/UseTheForce/doForces.F90,
186          src/UseTheForce/DarkSide/LJ.F90, src/UseTheForce/DarkSide/eam.F90,
# Line 30 | Line 196
196          src/math/erfc.F90, src/utils/interpolation.F90: Getting fortran
197          side prepped for single precision...
198  
199 < 2006-05-17 09:03  chrisfen
199 > 2006-05-17 10:03  chrisfen
200  
201          * samples/water/ssd-ion/ssdCl.md,
202          src/UseTheForce/DarkSide/electrostatic.F90: electrostatic
203          refinement
204  
205 < 2006-05-16 22:03  gezelter
205 > 2006-05-16 23:03  gezelter
206  
207          * configure, ac-tools/OOPSE.m4, make/Makefile.in: zlib fixes
208  
209 < 2006-05-16 15:38  gezelter
209 > 2006-05-16 16:38  gezelter
210  
211          * configure, ac-tools/OOPSE.m4, ac-tools/config.guess,
212          ac-tools/config.sub, ac-tools/configure.in, ac-tools/install-sh,
# Line 50 | Line 216
216          src/applications/staticProps/StaticProps.cpp: Autoconf fixes for
217          FFTW.  Multiple FFTW version support.
218  
219 < 2006-05-15 21:06  gezelter
219 > 2006-05-15 22:06  gezelter
220  
221          * README, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
222          make/Makefile.in, src/config.h.in,
# Line 66 | Line 232
232          src/integrators/LDForceManager.hpp, src/math/SquareMatrix.hpp,
233          src/utils/HydroProps.hpp: [no log message]
234  
235 < 2006-05-12 16:34  xsun
235 > 2006-05-12 17:34  xsun
236  
237          * src/applications/staticProps/: Hxy.cpp, Hxy.hpp, Makefile,
238          StaticProps.cpp, StaticPropsCmd.c, StaticPropsCmd.h: Changes to
239          calculate undulation spectrum
240  
241 < 2006-05-09 20:44  tim
241 > 2006-05-09 21:44  tim
242  
243          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
244          applications/dump2Xyz/Dump2XYZ.ggo,
# Line 82 | Line 248
248          visitors/AtomVisitor.cpp, visitors/AtomVisitor.hpp: adding a
249          gay-berne switch to Dump2XYZ
250  
251 < 2006-05-05 12:58  gezelter
251 > 2006-05-05 13:58  gezelter
252  
253          * src/UseTheForce/DarkSide/qpole.F90: Adding qpole
254  
255 < 2006-05-05 09:34  tim
255 > 2006-05-05 10:34  tim
256  
257          * ac-tools/aclocal.m4: finding ifort arguments that won't die under
258          two different versions of the intel fortran compiler
259  
260 < 2006-05-03 08:15  chrisfen
260 > 2006-05-03 09:15  chrisfen
261  
262          * src/applications/randomBuilder/Makefile: missing makefile was
263          hanging up 'make clean'
264  
265 < 2006-04-25 17:59  chuckv
265 > 2006-04-25 18:59  chuckv
266  
267          * src/applications/randomBuilder/: randomBuilder.cpp,
268          randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added
269          random builder to cvs.
270  
271 < 2006-04-25 17:54  chuckv
271 > 2006-04-25 18:54  chuckv
272  
273          * src/applications/nanoparticleBuilder/nanoparticleBuilder.cpp:
274          Change in siminfo used in nanoparticleBuilder.
275  
276 < 2006-04-25 17:30  chuckv
276 > 2006-04-25 18:30  chuckv
277  
278          * make/Makefile.in: Added random builder
279  
280 < 2006-04-25 17:29  chuckv
280 > 2006-04-25 18:29  chuckv
281  
282          * src/applications/simpleBuilder/: Makefile, randomBuilder.cpp,
283          randomBuilder.ggo, randomBuilderCmd.c, randomBuilderCmd.h: Added a
284          random builder to oopse.
285  
286 < 2006-04-25 08:35  gezelter
286 > 2006-04-25 09:35  gezelter
287  
288          * src/applications/hydrodynamics/: BeadModel.cpp, BeadModel.hpp,
289          ShapeBuilder.cpp, ShapeBuilder.hpp: Using OpenBabel element table
290          to pick vdw radii for hydrodynamics if the LJ sigma can't be found.
291  
292 < 2006-04-24 21:09  gezelter
292 > 2006-04-24 22:09  gezelter
293  
294          * configure, ac-tools/aclocal.m4, src/UseTheForce/DarkSide/LJ.F90,
295          src/applications/hydrodynamics/Hydro.cpp, src/brains/Register.cpp,
# Line 135 | Line 301
301          src/io/Globals.hpp, src/primitives/StuntDouble.hpp: Adding
302          spherical boundary conditions to LD integrator
303  
304 < 2006-04-24 21:06  gezelter
304 > 2006-04-24 22:06  gezelter
305  
306          * src/applications/hydrodynamics/: BeadModel.cpp, ShapeBuilder.cpp:
307          Added EAM atom types to Hydro models
308  
309 < 2006-04-21 15:02  chrisfen
309 > 2006-04-21 16:02  chrisfen
310  
311          * src/UseTheForce/DarkSide/eam.F90: put spline subroutines in the
312          EAM module
313  
314 < 2006-04-21 14:32  chrisfen
314 > 2006-04-21 15:32  chrisfen
315  
316          * ChangeLog, samples/shape/5CB.shape, samples/shape/8CB.shape,
317          samples/shape/C60.shape, samples/shape/C70.shape,
# Line 164 | Line 330
330          water samples to use shifted_force.  Probably should set the
331          defaults to use the damped version now that we sped it up.
332  
333 < 2006-04-20 22:19  chrisfen
333 > 2006-04-20 23:19  chrisfen
334  
335          * samples/water/spce/spce.md,
336          src/UseTheForce/DarkSide/electrostatic.F90: Electrosplines added...
337  
338 < 2006-04-20 16:02  chrisfen
338 > 2006-04-20 17:02  chrisfen
339  
340          * samples/argon/500.md, src/UseTheForce/DarkSide/sticky.F90,
341          src/UseTheForce/DarkSide/switcheroo.F90: splined up sticky
342  
343 < 2006-04-20 13:24  gezelter
343 > 2006-04-20 14:24  gezelter
344  
345          * samples/metals/EAM/Au_bulk_voter.md,
346          samples/metals/Sutton-Chen/Au_bulk_SC.md,
# Line 189 | Line 355
355          src/utils/interpolation.F90: Complete rewrite of spline code and
356          everything that uses it.
357  
358 < 2006-04-17 16:49  gezelter
358 > 2006-04-17 17:49  gezelter
359  
360          * configure, ac-tools/aclocal.m4, samples/argon/500.md,
361          samples/metals/EAM/Au_bulk_voter.md,
# Line 207 | Line 373
373          src/mdParser/SimplePreprocessor.hpp, src/types/DataHolder.hpp,
374          src/utils/interpolation.F90: Many performance improvements
375  
376 < 2006-04-15 21:51  chrisfen
376 > 2006-04-15 22:51  chrisfen
377  
378          * configure, samples/argon/500.md, src/UseTheForce/doForces.F90,
379          src/UseTheForce/fSwitchingFunction.h,
# Line 215 | Line 381
381          src/UseTheForce/DarkSide/switcheroo.F90: added a cubic spline to
382          switcheroo
383  
384 < 2006-04-15 16:58  chrisfen
384 > 2006-04-15 17:58  chrisfen
385  
386          * src/utils/Makefile.in: Since status.F90 is used by
387          interpolation.F90, the former needs to be listed above the later in
388          the Makefile.
389  
390 < 2006-04-14 16:59  gezelter
390 > 2006-04-14 17:59  gezelter
391  
392          * src/utils/interpolation.F90: changed the interface a bit
393  
394 < 2006-04-14 16:49  gezelter
394 > 2006-04-14 17:49  gezelter
395  
396          * src/utils/interpolation.F90: added some logical flags
397  
398 < 2006-04-14 16:06  chrisfen
398 > 2006-04-14 17:06  chrisfen
399  
400          * src/utils/interpolation.F90: Wiped the spline with derivatives
401          and corrected a boundary comparision error by eliminating the
402          check.  This algorithm REQUIRES known first derivatives at the
403          endpoints.
404  
405 < 2006-04-14 15:04  gezelter
405 > 2006-04-14 16:04  gezelter
406  
407          * src/utils/: Makefile.in, interpolation.F90: bug fixes for
408          interpolation module
409  
410 < 2006-04-14 14:57  gezelter
410 > 2006-04-14 15:57  gezelter
411  
412          * src/utils/interpolation.F90: Heavily modified interpolation
413          module, also moved to "utils"
414  
415 < 2006-04-12 16:15  chuckv
415 > 2006-04-12 17:15  chuckv
416  
417          * src/UseTheForce/DarkSide/interpolation.F90: Added interpolation
418          module.
419  
420 < 2006-04-11 10:33  gezelter
420 > 2006-04-11 11:33  gezelter
421  
422          * src/applications/staticProps/: StaticProps.ggo, StaticPropsCmd.c,
423          StaticPropsCmd.h: [no log message]
424  
425 < 2006-04-03 10:37  chuckv
425 > 2006-04-03 11:37  chuckv
426  
427          * configure, ac-tools/aclocal.m4, make/Makefile.in,
428          src/UseTheForce/DarkSide/simParallel.F90: Added status module to
# Line 1407 | Line 1573
1573  
1574          * make/Makefile.in, src/applications/atom2mdin/Makefile,
1575          src/applications/atom2mdin/atom2mdin.cpp,
1576 +        src/applications/mdinConverter/Makefile,
1577 +        src/applications/mdinConverter/mdinConverter.cpp,
1578          src/openbabel/oopseformat.cpp, src/openbabel/oopseformat.hpp:
1579          rename mdinConverter to atom2mdin
1580  
# Line 1471 | Line 1639
1639          UseTheForce/SC_FF.cpp, utils/ParameterManager.hpp: ForceField
1640          optional parameters....
1641  
1642 + 2005-11-16 16:24  tim
1643 +
1644 +        * src/applications/mdinConverter/: Makefile, mdinConverter.cpp:
1645 +        adding mdinConverter
1646 +
1647   2005-11-16 16:22  tim
1648  
1649          * src/openbabel/: Makefile, amberformat.cpp, amberformat.hpp,
# Line 1725 | Line 1898
1898          * src/UseTheForce/DarkSide/: fInteractionMap.h, suttonchen.F90: In
1899          process of adding sutton-chen forcefield.
1900  
1901 < 2005-10-26 18:32  chrisfen
1901 > 2005-10-26 19:32  chrisfen
1902  
1903          * src/brains/SimInfo.cpp: changed the default switching radius to
1904          85% of rcut
1905  
1906 < 2005-10-26 18:31  chrisfen
1906 > 2005-10-26 19:31  chrisfen
1907  
1908          * src/UseTheForce/DarkSide/electrostatic.F90: reaction field looks
1909          to be working now - for charges and dipoles alike
1910  
1911 < 2005-10-26 18:31  chrisfen
1911 > 2005-10-26 19:31  chrisfen
1912  
1913          * src/UseTheForce/doForces.F90: reaction field looks to be working
1914          now
1915  
1916 < 2005-10-26 18:30  chrisfen
1916 > 2005-10-26 19:30  chrisfen
1917  
1918          * samples/water/ssdrf/water.md: added a test molecule
1919  
1920 < 2005-10-26 18:30  chrisfen
1920 > 2005-10-26 19:30  chrisfen
1921  
1922          * forceFields/DUFF2.frc: added a test atom type
1923  
1924 < 2005-10-24 09:06  chrisfen
1924 > 2005-10-24 10:06  chrisfen
1925  
1926          * src/UseTheForce/DarkSide/electrostatic.F90: added charge-dipole
1927          reaction field - don't know if it works...
1928  
1929 < 2005-10-23 16:08  chrisfen
1929 > 2005-10-23 17:08  chrisfen
1930  
1931          * src/: UseTheForce/doForces.F90,
1932          UseTheForce/DarkSide/electrostatic.F90, primitives/RigidBody.cpp:
# Line 1761 | Line 1934
1934          added reaction field for charges - still need to do charge-dipole
1935          RF
1936  
1937 < 2005-10-23 16:07  chrisfen
1937 > 2005-10-23 17:07  chrisfen
1938  
1939          * samples/water/ssdrf/ssdrf.md: minor changes when testing reaction
1940          field
1941  
1942 < 2005-10-23 16:06  chrisfen
1942 > 2005-10-23 17:06  chrisfen
1943  
1944          * samples/water/spce/spce.md: reaction field now works for charges
1945  
1946 < 2005-10-20 15:27  tim
1946 > 2005-10-20 16:27  tim
1947  
1948          * src/primitives/Torsion.cpp: Fix the other branch of force
1949          calculation in Torision.cpp
1950  
1951 < 2005-10-19 14:24  chrisfen
1951 > 2005-10-19 15:24  chrisfen
1952  
1953          * src/: UseTheForce/doForces.F90,
1954          UseTheForce/DarkSide/electrostatic.F90,
# Line 1783 | Line 1956
1956          brains/ForceManager.cpp, brains/SimInfo.cpp: Still had some globals
1957          toUpper problems - these changes should fix those...
1958  
1959 < 2005-10-19 14:23  chrisfen
1959 > 2005-10-19 15:23  chrisfen
1960  
1961          * samples/water/ssdrf/ssdrf.md: nothing
1962  
1963 < 2005-10-19 12:03  gezelter
1963 > 2005-10-19 13:03  gezelter
1964  
1965          * src/UseTheForce/DarkSide/gb.F90: fixed an MPI compilation bug in
1966          GayBerne
1967  
1968 < 2005-10-19 11:49  tim
1968 > 2005-10-19 12:49  tim
1969  
1970          * src/: UseTheForce/DarkSide/fInteractionMap.h,
1971          brains/ForceManager.cpp: fix an index mismathcing between c and
1972          fortran
1973  
1974 < 2005-10-18 18:03  gezelter
1974 > 2005-10-18 19:03  gezelter
1975  
1976          * samples/cutoff/: lj.md, max.md, mix.md, traditional.md: added
1977          samples for the cutoff methods that Yang Zheng has been working on
1978  
1979 < 2005-10-18 16:13  gezelter
1979 > 2005-10-18 17:13  gezelter
1980  
1981          * src/UseTheForce/DarkSide/gb.F90: fixed gb/lj and gb/gb torques
1982          and a rotation matrix bug
1983  
1984 < 2005-10-18 16:13  gezelter
1984 > 2005-10-18 17:13  gezelter
1985  
1986          * samples/gbljtest/: 2gb.in, 2gb.md, gb.md, gb2lj1.in, gb2lj1.md,
1987          gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md:
1988          added a few GB test cases
1989  
1990 < 2005-10-18 16:13  gezelter
1990 > 2005-10-18 17:13  gezelter
1991  
1992          * forceFields/DUFF2.frc: Fixing GB parameters
1993  
1994 < 2005-10-18 13:36  kdaily
1994 > 2005-10-18 14:36  kdaily
1995  
1996          * forceFields/DUFF2.frc: Changed the parameters for the Gay-Berne
1997          type
1998  
1999 < 2005-10-18 10:01  chrisfen
1999 > 2005-10-18 11:01  chrisfen
2000  
2001          * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90,
2002          UseTheForce/DarkSide/Makefile,
# Line 1833 | Line 2006
2006          UseTheForce/DarkSide/reactionField.F90, brains/SimInfo.cpp: merged
2007          reaction field with electrostatics.F90
2008  
2009 < 2005-10-17 18:13  tim
2009 > 2005-10-17 19:13  tim
2010  
2011          * src/: brains/ForceManager.cpp, brains/Stats.cpp,
2012          brains/Stats.hpp, integrators/VelocityVerletIntegrator.cpp,
2013          io/BASS_interface.h, io/Globals.cpp, io/StatWriter.cpp,
2014          io/StatWriter.hpp: Customized StatWriter is working
2015  
2016 < 2005-10-17 17:42  kdaily
2016 > 2005-10-17 18:42  kdaily
2017  
2018          * src/UseTheForce/DarkSide/gb.F90: using notation from Cleaver
2019          paper
2020  
2021 < 2005-10-17 16:47  gezelter
2021 > 2005-10-17 17:47  gezelter
2022  
2023          * src/UseTheForce/DarkSide/gb.F90: bugtracking gb
2024  
2025 < 2005-10-17 14:24  tim
2025 > 2005-10-17 15:24  tim
2026  
2027          * src/io/ParamConstraint.hpp: Another bug fix
2028  
2029 < 2005-10-17 14:22  tim
2029 > 2005-10-17 15:22  tim
2030  
2031          * src/io/: Globals.hpp, ParamConstraint.hpp: fix some namespace
2032          issues in Globals
2033  
2034 < 2005-10-17 14:12  gezelter
2034 > 2005-10-17 15:12  gezelter
2035  
2036          * src/: UseTheForce/DUFF.cpp, UseTheForce/doForces.F90,
2037          UseTheForce/DarkSide/Makefile, UseTheForce/DarkSide/gb.F90,
# Line 1868 | Line 2041
2041          types/DirectionalAtomType.cpp, types/DirectionalAtomType.hpp:
2042          changing GB architecture
2043  
2044 < 2005-10-17 14:12  gezelter
2044 > 2005-10-17 15:12  gezelter
2045  
2046          * samples/gbljtest/: gbRotRoundX.in, gbRotRoundY.in,
2047          gbRotRoundZ.in: Adding samples for gb tests
2048  
2049 < 2005-10-16 22:06  tim
2049 > 2005-10-16 23:06  tim
2050  
2051          * src/io/: Globals.cpp, Globals.hpp: fix a seg fault when try copy
2052          a  string to event's err_msg, there are still tons of memory
2053          leaking problem in Globals
2054  
2055 < 2005-10-16 19:51  tim
2055 > 2005-10-16 20:51  tim
2056  
2057          * src/io/: Globals.cpp, Globals.hpp, ParamConstraint.hpp: Change
2058          error message in Globals
2059  
2060 < 2005-10-14 16:43  tim
2060 > 2005-10-14 17:43  tim
2061  
2062          * src/io/: Globals.cpp, ParamConstraint.hpp: Constraints for
2063          parameters are working now
2064  
2065 < 2005-10-14 11:43  gezelter
2065 > 2005-10-14 12:43  gezelter
2066  
2067          * samples/gbljtest/: gb.md, lj.md: Adding .md files for GB/LJ tests
2068  
2069 < 2005-10-14 11:05  gezelter
2069 > 2005-10-14 12:05  gezelter
2070  
2071          * samples/gbljtest/: gbRotRoundX.in, gbRotRoundX.md,
2072          gbRotRoundY.in, gbRotRoundY.md, gbRotRoundZ.in, gbRotRoundZ.md:
2073          Adding some Gay Berne tests
2074  
2075 < 2005-10-14 11:05  gezelter
2075 > 2005-10-14 12:05  gezelter
2076  
2077          * samples/cutoff/: cutoff_test.in, cutoff_test.md: Adding some
2078          cutoff tests
2079  
2080 < 2005-10-14 10:44  kdaily
2080 > 2005-10-14 11:44  kdaily
2081  
2082          * forceFields/DUFF2.frc, src/UseTheForce/DUFF.cpp,
2083          src/UseTheForce/doForces.F90, src/UseTheForce/DarkSide/gb.F90,
# Line 1912 | Line 2085
2085          src/UseTheForce/DarkSide/gb_interface.h: Add parts for the GayBerne
2086          LJ
2087  
2088 < 2005-10-14 09:48  tim
2088 > 2005-10-14 10:48  tim
2089  
2090          * src/io/ParamConstraint.hpp: Adding Parameter Constraint class
2091  
2092 < 2005-10-14 09:18  chrisfen
2092 > 2005-10-14 10:18  chrisfen
2093  
2094          * samples/thermoIntegration/liquid/ssde.md,
2095          samples/thermoIntegration/solid/ssde.md, src/io/Globals.cpp,
2096          src/restraints/Restraints.cpp: added default restraint spring
2097          constants into Globals
2098  
2099 < 2005-10-13 17:26  tim
2099 > 2005-10-13 18:26  tim
2100  
2101          * src/: applications/oopse/oopse.cpp, brains/ForceManager.cpp,
2102          brains/SimCreator.cpp, brains/SimInfo.cpp, brains/Snapshot.hpp,
# Line 1935 | Line 2108
2108          restraints/ThermoIntegrationForceManager.cpp,
2109          visitors/ZconsVisitor.cpp: rewrite Globals
2110  
2111 < 2005-10-12 16:57  chuckv
2111 > 2005-10-12 17:57  chuckv
2112  
2113          * src/brains/ForceManager.cpp: Fix to forceManager to pass
2114          potential array to fortran.
2115  
2116 < 2005-10-12 16:00  gezelter
2116 > 2005-10-12 17:00  gezelter
2117  
2118          * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: Don't
2119          remember what we did
2120  
2121 < 2005-10-12 16:00  gezelter
2121 > 2005-10-12 17:00  gezelter
2122  
2123          * src/UseTheForce/: doForces.F90, doForces_interface.F90,
2124          DarkSide/LJ.F90, DarkSide/eam.F90, DarkSide/fInteractionMap.h,
2125          DarkSide/force_globals.F90, DarkSide/gb.F90, DarkSide/shapes.F90,
2126          DarkSide/sticky.F90: simplifying long range potential array
2127  
2128 < 2005-10-12 16:00  gezelter
2128 > 2005-10-12 17:00  gezelter
2129  
2130          * samples/cutoff/: cutoff_test.in, cutoff_test.md: Testing new
2131          cutoff methods
2132  
2133 < 2005-10-12 16:00  gezelter
2133 > 2005-10-12 17:00  gezelter
2134  
2135          * forceFields/DUFF2.frc: Messing with 2-point water models
2136  
2137 < 2005-10-12 15:22  chuckv
2137 > 2005-10-12 16:22  chuckv
2138  
2139          * src/UseTheForce/doForces_interface.F90: Breaky, Breaky: c-fortran
2140          interface now expects an array for pot.
2141  
2142 < 2005-10-12 15:18  chuckv
2142 > 2005-10-12 16:18  chuckv
2143  
2144          * src/UseTheForce/: doForces.F90, DarkSide/gb.F90,
2145          DarkSide/shapes.F90, DarkSide/sticky.F90: More Change goodness for
2146          calculation of potential.
2147  
2148 < 2005-10-12 14:55  chuckv
2148 > 2005-10-12 15:55  chuckv
2149  
2150          * src/UseTheForce/doForces.F90: More changes to MPI potential
2151          calculations.
2152  
2153 < 2005-10-12 13:59  chuckv
2153 > 2005-10-12 14:59  chuckv
2154  
2155          * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90,
2156          DarkSide/eam.F90, DarkSide/electrostatic.F90,
# Line 1985 | Line 2158
2158          DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: Breaky
2159          Breaky: Add Support for seperating potential contributions.
2160  
2161 < 2005-10-11 17:00  chuckv
2161 > 2005-10-11 18:00  chuckv
2162  
2163          * src/UseTheForce/doForces.F90: Free some variables that weren't
2164          freed before.
2165  
2166 < 2005-10-11 16:59  chuckv
2166 > 2005-10-11 17:59  chuckv
2167  
2168          * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
2169          GeometryCreator.hpp, GeometryFactory.cpp: Design change for nanoRod
2170          builder --twinned.
2171  
2172 < 2005-10-11 16:57  chuckv
2172 > 2005-10-11 17:57  chuckv
2173  
2174          * src/applications/nanoparticleBuilder/: nanoparticleBuilder.cpp,
2175          nanoparticleBuilder.ggo, nanoparticleBuilderCmd.c,
# Line 2004 | Line 2177
2177          sphericalNanoparticle.hpp: Added code for nanoparticle builder to
2178          cvs.
2179  
2180 < 2005-10-10 16:34  chuckv
2180 > 2005-10-10 17:34  chuckv
2181  
2182          * src/UseTheForce/doForces.F90: Bug fix, undeclared local variable
2183          in MPI.
2184  
2185 < 2005-10-10 16:20  chuckv
2185 > 2005-10-10 17:20  chuckv
2186  
2187          * src/UseTheForce/doForces.F90: Fixed MPI bug with Row and Column
2188          indexing of groupToGtype. We now have two seperate maps
2189          groupToGtypeRow and groupToGypeCol. GroupToGtypeCol is a pointer
2190          that is set to groupToGtypeRow in the single processor version.
2191  
2192 < 2005-10-06 13:44  chrisfen
2192 > 2005-10-06 14:44  chrisfen
2193  
2194          * samples/water/: dimer/water.md, spce/water.md, ssd/water.md,
2195          ssd-ion/water.md, ssde/water.md, ssdrf/water.md, tap/water.md,
2196          tip3p_ice/water.md, tip4p/water.md: fixing up the samples
2197  
2198 < 2005-10-05 16:12  tim
2198 > 2005-10-05 17:12  tim
2199  
2200          * src/primitives/RigidBody.cpp: There is still something wrong with
2201          inertia tensor projection
2202  
2203 < 2005-10-05 14:35  tim
2203 > 2005-10-05 15:35  tim
2204  
2205          * src/primitives/RigidBody.cpp: erase output of inertia tensor.
2206          There is still something wrong with current implementation.
2207  
2208 < 2005-10-05 14:34  tim
2208 > 2005-10-05 15:34  tim
2209  
2210          * src/brains/MoleculeCreator.cpp: fix a bug in creating
2211          cutoffGroup. When cutoffGroup is turned off, there is a mismatch
2212          between group and center of mass array
2213  
2214 < 2005-10-05 14:12  tim
2214 > 2005-10-05 15:12  tim
2215  
2216          * src/primitives/RigidBody.cpp: fix a bug in creating cutoffGroup.
2217          When cutoffGroup is turned off, there is a mismatch between group
2218          and center of mass array
2219  
2220 < 2005-10-04 14:34  chrisfen
2220 > 2005-10-04 15:34  chrisfen
2221  
2222          * src/brains/: ForceManager.cpp, SimInfo.cpp: fixed an annoying
2223          mass ratio bug that results in simulation failure with massless
2224          particles
2225  
2226 < 2005-10-04 14:33  chrisfen
2226 > 2005-10-04 15:33  chrisfen
2227  
2228          * src/UseTheForce/DarkSide/electrostatic.F90: maybe some work on
2229          wolf
2230  
2231 < 2005-10-04 14:32  chrisfen
2231 > 2005-10-04 15:32  chrisfen
2232  
2233          * samples/water/dimer/two.md, samples/water/dimer/water.md,
2234          samples/water/tip3p_ice/tp3.md, samples/water/tip3p_ice/water.md,
2235          samples/water/tip4p/tp4.md, src/UseTheForce/doForces.F90: just some
2236          random changes when testing
2237  
2238 < 2005-10-03 10:54  tim
2238 > 2005-10-03 11:54  tim
2239  
2240          * src/primitives/: DirectionalAtom.cpp, RigidBody.cpp: fix a bug in
2241          projecting the inertia tensor of directional atom in rigibody into
2242          rigidbody's body frame (previous commit is wrong)
2243  
2244 < 2005-10-03 09:31  tim
2244 > 2005-10-03 10:31  tim
2245  
2246          * src/primitives/RigidBody.cpp: fix a bug in projecting the inertia
2247          tensor of directional atom in rigibody into rigidbody's body frame
2248  
2249 < 2005-09-28 13:47  chrisfen
2249 > 2005-09-28 14:47  chrisfen
2250  
2251          * src/UseTheForce/DarkSide/electrostatic.F90: working on wolf
2252  
2253 < 2005-09-28 13:46  chrisfen
2253 > 2005-09-28 14:46  chrisfen
2254  
2255          * samples/water/: dimer/cl.md, dimer/mix.md, dimer/mix2.md,
2256          dimer/ssd.md, dimer/tap.md, dimer/two.md, spce/spce.md, ssd/ssd.md,
2257          ssd-ion/ssdCl.md, ssde/ssde.md, tap/tap.md, tip3p_ice/tp3.md,
2258          tip4p/tp4.md: fixed some samples
2259  
2260 < 2005-09-28 13:46  chrisfen
2260 > 2005-09-28 14:46  chrisfen
2261  
2262          * ChangeLog: updated
2263  
2264 < 2005-09-28 11:55  tim
2264 > 2005-09-28 12:55  tim
2265  
2266          * src/math/SquareMatrix3.hpp: using epsilon instead of 0.0 to avoid
2267          divergence in rotation matrix to quaternion transformation
2268  
2269 < 2005-09-28 11:32  gezelter
2269 > 2005-09-28 12:32  gezelter
2270  
2271          * src/primitives/RigidBody.cpp: Rotation matrix multiplication
2272          order error
2273  
2274 < 2005-09-28 11:32  gezelter
2274 > 2005-09-28 12:32  gezelter
2275  
2276          * src/io/DumpReader.cpp: tracking down quaternion bug
2277  
2278 < 2005-09-28 11:32  gezelter
2278 > 2005-09-28 12:32  gezelter
2279  
2280          * forceFields/DUFF2.frc: Added DIP atom types for 2-point water
2281          model
2282  
2283 < 2005-09-27 15:02  tim
2283 > 2005-09-27 16:02  tim
2284  
2285          * src/math/SquareMatrix3.hpp: fix a bug in convert rotation matrix
2286          to quaternion
2287  
2288 < 2005-09-26 13:38  chuckv
2288 > 2005-09-26 14:38  chuckv
2289  
2290          * src/UseTheForce/DarkSide/electrostatic.F90: Added define for ifc
2291          7 so derfc is external. Other compilers should treat erfc as
2292          intrinsic.
2293  
2294 < 2005-09-26 12:07  chuckv
2294 > 2005-09-26 13:07  chuckv
2295  
2296          * src/UseTheForce/DarkSide/electrostatic.F90: Changed erfc to derfc
2297          and declared it to be external to fix issure with ifc7. Hopefully
2298          this will not cause a problem with other compilers where derfc is
2299          an intrinsic function.
2300  
2301 < 2005-09-26 11:42  chuckv
2301 > 2005-09-26 12:42  chuckv
2302  
2303          * src/UseTheForce/DarkSide/simulation.F90: MPI fix for SimHasAtype
2304          in simulation module. We needed a seperate receive buffer.
2305  
2306 < 2005-09-26 10:58  chuckv
2306 > 2005-09-26 11:58  chuckv
2307  
2308          * src/: brains/SimInfo.cpp, io/Globals.cpp, io/Globals.hpp: Added
2309          support for skinThickness keyword to Globals.
2310  
2311 < 2005-09-26 10:56  tim
2311 > 2005-09-26 11:56  tim
2312  
2313          * src/io/DumpReader.cpp: fix a typo in DumpReader
2314  
2315 < 2005-09-26 09:27  chrisfen
2315 > 2005-09-26 10:27  chrisfen
2316  
2317          * samples/: minimizer/tip4p_two.md,
2318          thermoIntegration/liquid/ssde.md, thermoIntegration/solid/ssde.md,
# Line 2149 | Line 2322
2322          water/ssde/ssde.md, water/tap/tap.md, water/tip3p_ice/tp3.md,
2323          water/tip4p/tp4.md: fixing up some samples
2324  
2325 < 2005-09-24 12:39  chrisfen
2325 > 2005-09-24 13:39  chrisfen
2326  
2327          * src/UseTheForce/DarkSide/electrostatic.F90: slowdown fixed - now
2328          roughly the same speed as the old version when using dipoles
# Line 2157 | Line 2330
2330          energies are now exactly the same between the old version of OOPSE
2331          and this version
2332  
2333 < 2005-09-24 12:38  chrisfen
2333 > 2005-09-24 13:38  chrisfen
2334  
2335          * samples/water/ssdrf/ssdrf.md: turned rf on
2336  
2337 < 2005-09-23 15:31  chuckv
2337 > 2005-09-23 16:31  chuckv
2338  
2339          * src/UseTheForce/doForces.F90: Fixed "dum-dum" where we ignore the
2340          skin thickness and hardcode listSkin to be 1.0. We now get listskin
2341          from skin. This will get fixed to where we can manually set skin
2342          thickness.
2343  
2344 < 2005-09-22 13:50  gezelter
2344 > 2005-09-22 14:50  gezelter
2345  
2346          * src/math/derfc.F90: added error function
2347  
2348 < 2005-09-21 19:08  chuckv
2348 > 2005-09-21 20:08  chuckv
2349  
2350          * src/integrators/Velocitizer.cpp: Removed print statement for
2351          angular momentum and inertia tensor from velocitizer.
2352  
2353 < 2005-09-21 19:04  chuckv
2353 > 2005-09-21 20:04  chuckv
2354  
2355          * src/integrators/Velocitizer.cpp: Removed print statements for
2356          remove angular momentum.
2357  
2358 < 2005-09-21 18:45  chuckv
2358 > 2005-09-21 19:45  chuckv
2359  
2360          * src/UseTheForce/DarkSide/LJ.F90: Bug fix: If we are not using LJ
2361          (say we are using EAM), we probably shouldn't rebuild the LJ mixing
2362          map.
2363  
2364 < 2005-09-21 15:59  tim
2364 > 2005-09-21 16:59  tim
2365  
2366          * src/io/: DumpReader.cpp, DumpReader.hpp, DumpWriter.cpp:
2367          DumpReader using pure c++ io
2368  
2369 < 2005-09-21 12:20  chrisfen
2369 > 2005-09-21 13:20  chrisfen
2370  
2371          * src/UseTheForce/: doForces.F90, DarkSide/LJ.F90: Fixed a
2372          defaultCutoff bug (HEMES!)
2373  
2374 < 2005-09-20 17:13  gezelter
2374 > 2005-09-20 18:13  gezelter
2375  
2376          * make/Makefile.in: libz additions
2377  
2378 < 2005-09-20 17:03  gezelter
2378 > 2005-09-20 18:03  gezelter
2379  
2380          * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
2381          src/config.h.in: added check for zlib in configure
2382  
2383 < 2005-09-20 16:22  tim
2383 > 2005-09-20 17:22  tim
2384  
2385          * src/io/: DumpWriter.cpp, DumpWriter.hpp, Makefile, gzstream.cpp,
2386          gzstream.hpp, zipstream.hpp: adding zlib support for DumpWriter
2387  
2388 < 2005-09-20 11:22  tim
2388 > 2005-09-20 12:22  tim
2389  
2390          * test/io/: ZipstreamTestCase.cpp, ZipstreamTestCase.hpp: adding
2391          testcase for zipstream
2392  
2393 < 2005-09-20 10:41  tim
2393 > 2005-09-20 11:41  tim
2394  
2395          * src/io/zipstream.hpp: adding zipstream.hpp
2396  
2397 < 2005-09-20 10:34  chrisfen
2397 > 2005-09-20 11:34  chrisfen
2398  
2399          * samples/: dipole/splitInWater.md, dipole/split_SSD.md,
2400          dipole/twoSplitDipole.md, minimizer/ssdEM.md,
2401          minimizer/tip4p_two.md, water/ssdrf/ssdrf.md, zcons/zconsFixed.md,
2402          zcons/zconsMoving.md: fixed up some sample md files
2403  
2404 < 2005-09-19 18:21  chrisfen
2404 > 2005-09-19 19:21  chrisfen
2405  
2406          * ChangeLog, samples/water/ssdrf/ssdrf.md,
2407          src/UseTheForce/doForces.F90,
# Line 2237 | Line 2410
2410          src/brains/fSimulation.h: Fixed bugs in reaction field, now it
2411          appears as though it really is working...
2412  
2413 < 2005-09-18 15:45  chrisfen
2413 > 2005-09-18 16:45  chrisfen
2414  
2415          * ChangeLog, samples/water/ssdrf/ssdrf.md,
2416          src/UseTheForce/doForces.F90,
# Line 2248 | Line 2421
2421          src/brains/SimInfo.cpp: reaction field seems to work now, still
2422          need to do some testing...
2423  
2424 < 2005-09-16 18:04  chuckv
2424 > 2005-09-16 19:04  chuckv
2425  
2426          * src/io/: Globals.cpp, Globals.hpp: Added keywords for compressed
2427          dump files.
2428  
2429 < 2005-09-16 16:07  chrisfen
2429 > 2005-09-16 17:07  chrisfen
2430  
2431          * src/: UseTheForce/doForces_interface.F90,
2432          UseTheForce/doForces_interface.h, brains/SimInfo.cpp: xlf found a
2433          bug that ifc missed...
2434  
2435 < 2005-09-16 15:36  chrisfen
2435 > 2005-09-16 16:36  chrisfen
2436  
2437          * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90:
2438          fixing some summation method issues
2439  
2440 < 2005-09-16 14:35  chrisfen
2440 > 2005-09-16 15:35  chrisfen
2441  
2442          * src/brains/SimInfo.cpp: fixed a capitalization error
2443  
2444 < 2005-09-16 14:34  chrisfen
2444 > 2005-09-16 15:34  chrisfen
2445  
2446          * src/UseTheForce/: fElectrostaticSummationMethod.h,
2447          DarkSide/fElectrostaticSummationMethod.h: moved a header file
2448          around
2449  
2450 < 2005-09-16 14:00  chrisfen
2450 > 2005-09-16 15:00  chrisfen
2451  
2452          * src/: UseTheForce/DarkSide/electrostatic_interface.F90,
2453          brains/SimInfo.cpp, brains/SimInfo.hpp: it builds now, but there
2454          are known issues - particularly with reaction field...
2455  
2456 < 2005-09-16 11:07  chrisfen
2456 > 2005-09-16 12:07  chrisfen
2457  
2458          * src/: UseTheForce/DarkSide/electrostatic.F90, brains/SimInfo.cpp,
2459          io/Globals.cpp, io/Globals.hpp: some fixes but even more breaking
2460          (cutting out the old way to do reaction field)
2461  
2462 < 2005-09-15 17:05  gezelter
2462 > 2005-09-15 18:05  gezelter
2463  
2464          * src/UseTheForce/: doForces.F90, fCoulombicCorrection.h,
2465          fElectrostaticSummationMethod.h, DarkSide/electrostatic.F90,
2466          DarkSide/electrostatic_interface.F90,
2467          DarkSide/electrostatic_interface.h: Working on adding WOLF
2468  
2469 < 2005-09-15 14:17  tim
2469 > 2005-09-15 15:17  tim
2470  
2471          * src/io/DumpReader.cpp: Fix a bug in DumpReader in case readFrame
2472          is called without calling getNFrames
2473  
2474 < 2005-09-15 08:47  chrisfen
2474 > 2005-09-15 09:47  chrisfen
2475  
2476          * src/UseTheForce/fCoulombicCorrection.h: forgot to add a header
2477  
2478 < 2005-09-14 21:48  chuckv
2478 > 2005-09-14 22:48  chuckv
2479  
2480          * src/UseTheForce/doForces.F90: Fixed bug where gtypeMaxCutoff was
2481          not initialized after creation. When maxval(gtypeMaxCutoff) was
2482          called, the largest random garbage value was returned from the
2483          array.
2484  
2485 < 2005-09-14 19:14  chrisfen
2485 > 2005-09-14 20:14  chrisfen
2486  
2487          * src/: brains/SimInfo.cpp, brains/SimInfo.hpp, io/Globals.cpp,
2488          io/Globals.hpp: changes to include the coulombicCorrection selector
2489  
2490 < 2005-09-14 19:13  chrisfen
2490 > 2005-09-14 20:13  chrisfen
2491  
2492          * src/UseTheForce/DarkSide/: Makefile, electrostatic.F90,
2493          reactionField.F90: added in the undamped wolf, in the process of
2494          doing the damped wolf
2495  
2496 < 2005-09-14 19:13  chrisfen
2496 > 2005-09-14 20:13  chrisfen
2497  
2498          * src/UseTheForce/: doForces.F90, doForces_interface.F90,
2499          doForces_interface.h, notifyCutoffs.F90: some changes to activate
2500          the coulombicCorrection selector
2501  
2502 < 2005-09-14 19:11  chrisfen
2502 > 2005-09-14 20:11  chrisfen
2503  
2504          * samples/water/dimer/: cl.in, cl.md, water.md: just some testing
2505  
2506 < 2005-09-14 19:11  chrisfen
2506 > 2005-09-14 20:11  chrisfen
2507  
2508          * samples/argon/: 500.in, 500.md: Equilibrated the sample
2509  
2510 < 2005-09-14 19:10  chrisfen
2510 > 2005-09-14 20:10  chrisfen
2511  
2512          * forceFields/DUFF2.frc: re-added Cl- and Na+
2513  
2514 < 2005-09-14 15:31  chuckv
2514 > 2005-09-14 16:31  chuckv
2515  
2516          * src/UseTheForce/DarkSide/eam.F90: EAM now uses eamlist to lookup
2517          eamAtypes instead of assuming a 1-1 correspondence to atypes.
2518  
2519 < 2005-09-14 15:28  gezelter
2519 > 2005-09-14 16:28  gezelter
2520  
2521          * src/UseTheForce/doForces.F90: fix to put back calculation of r in
2522          do_prepair
2523  
2524 < 2005-09-14 14:02  gezelter
2524 > 2005-09-14 15:02  gezelter
2525  
2526          * src/UseTheForce/DarkSide/LJ.F90: fixed a bug in the
2527          createMixingMap routine.  It should now set doShift correctly
2528  
2529 < 2005-09-07 17:44  chuckv
2529 > 2005-09-07 18:44  chuckv
2530  
2531          * src/UseTheForce/doForces.F90: Added nGroupsInRow for mpi build.
2532  
2533 < 2005-09-07 17:23  chuckv
2533 > 2005-09-07 18:23  chuckv
2534  
2535          * src/UseTheForce/DarkSide/simParallel.F90: Added access to mpi
2536          logical variables
2537  
2538 < 2005-09-07 17:08  gezelter
2538 > 2005-09-07 18:08  gezelter
2539  
2540          * src/UseTheForce/doForces.F90: bugfix on the grouptype finding
2541          algorithm
2542  
2543 < 2005-09-07 15:46  gezelter
2543 > 2005-09-07 16:46  gezelter
2544  
2545          * src/: UseTheForce/doForces.F90,
2546          UseTheForce/doForces_interface.F90, UseTheForce/notifyCutoffs.F90,
# Line 2376 | Line 2549
2549          io/Globals.cpp, io/Globals.hpp: adding c-side interface to change
2550          cutoff Policy
2551  
2552 < 2005-09-07 14:18  gezelter
2552 > 2005-09-07 15:18  gezelter
2553  
2554          * src/UseTheForce/doForces.F90: Some bug hunting
2555  
2556 < 2005-09-07 14:18  gezelter
2556 > 2005-09-07 15:18  gezelter
2557  
2558          * samples/argon/argonNVT.md: Just a longer test
2559  
2560 < 2005-09-06 12:32  chuckv
2560 > 2005-09-06 13:32  chuckv
2561  
2562          * src/UseTheForce/doForces.F90: Added allocation for gtypeCutoffmap
2563          etc..
2564  
2565 < 2005-09-01 17:56  gezelter
2565 > 2005-09-01 18:56  gezelter
2566  
2567          * src/UseTheForce/doForces.F90: initialized atomTypeMaxCutoff(i) to
2568          zero
2569  
2570 < 2005-09-01 15:17  gezelter
2570 > 2005-09-01 16:17  gezelter
2571  
2572          * src/UseTheForce/: doForces.F90, doForces_interface.F90: wrote
2573          createGtypeCutoffMap
2574  
2575 < 2005-08-30 13:23  chrisfen
2575 > 2005-08-30 14:23  chrisfen
2576  
2577          * src/: UseTheForce/doForces.F90,
2578          UseTheForce/doForces_interface.F90,
# Line 2409 | Line 2582
2582          brains/fSimulation.h, io/Globals.cpp, io/Globals.hpp: made some
2583          changes for implementing the wolf potential
2584  
2585 < 2005-08-26 17:39  chrisfen
2585 > 2005-08-26 18:39  chrisfen
2586  
2587          * src/UseTheForce/DarkSide/eam.F90: updated getEAMCut
2588  
2589 < 2005-08-26 16:30  chrisfen
2589 > 2005-08-26 17:30  chrisfen
2590  
2591          * src/UseTheForce/: doForces.F90, DarkSide/eam.F90,
2592          DarkSide/gb.F90, DarkSide/shapes.F90, DarkSide/sticky.F90: added
2593          some probably nonfunctional get*cut routines
2594  
2595 < 2005-08-26 15:34  chuckv
2595 > 2005-08-26 16:34  chuckv
2596  
2597          * src/UseTheForce/DarkSide/eam.F90: Added eamType map to atid map.
2598  
2599 < 2005-08-26 11:36  gezelter
2599 > 2005-08-26 12:36  gezelter
2600  
2601          * src/UseTheForce/doForces.F90: fixing some of the problems in the
2602          interactionHash and gtypeCutoff routines
2603  
2604 < 2005-08-17 10:26  gezelter
2604 > 2005-08-17 11:26  gezelter
2605  
2606          * src/UseTheForce/: doForces.F90, fCutoffPolicy.h,
2607          DarkSide/simulation.F90: added fCutoffPolicy.h
2608  
2609 < 2005-08-11 16:04  gezelter
2609 > 2005-08-11 17:04  gezelter
2610  
2611          * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: breakage in
2612          progress
2613  
2614 < 2005-08-10 14:17  gezelter
2614 > 2005-08-10 15:17  gezelter
2615  
2616          * src/primitives/StuntDouble.hpp: putting spaceballs back where
2617          they belong
2618  
2619 < 2005-08-09 17:33  gezelter
2619 > 2005-08-09 18:33  gezelter
2620  
2621          * src/UseTheForce/DarkSide/LJ.F90: Complete rewrite of Lennard
2622          Jones module
2623  
2624 < 2005-08-09 17:33  gezelter
2624 > 2005-08-09 18:33  gezelter
2625  
2626          * src/UseTheForce/doForces.F90: Breaky Breaky BREAKY breaky breaky
2627  
2628 < 2005-08-09 14:40  chuckv
2628 > 2005-08-09 15:40  chuckv
2629  
2630          * src/UseTheForce/doForces.F90: In process of re-write for group
2631          based cutoff....
2632  
2633 < 2005-07-29 14:38  gezelter
2633 > 2005-07-29 15:38  gezelter
2634  
2635          * src/UseTheForce/doForces.F90: fixes in progress
2636  
2637 < 2005-07-29 12:34  tim
2637 > 2005-07-29 13:34  tim
2638  
2639          * src/UseTheForce/doForces.F90: fix a bug which does not update
2640          me_i and me_j correctly
2641  
2642 < 2005-07-28 17:12  chuckv
2642 > 2005-07-28 18:12  chuckv
2643  
2644          * src/UseTheForce/: doForces.F90, notifyCutoffs.F90: Changed
2645          cutoffs... Segfaults nicely now...
2646  
2647 < 2005-07-20 12:04  gezelter
2647 > 2005-07-20 13:04  gezelter
2648  
2649          * configure, ac-tools/aclocal.m4: fixed ACX_MPI to ignore some text
2650          error messages from pathscale compiler
2651  
2652 < 2005-07-13 11:48  tim
2652 > 2005-07-13 12:48  tim
2653  
2654          * src/applications/staticProps/DensityPlot.cpp: std::bind2nd is in
2655          <functional>
2656  
2657 < 2005-07-13 10:54  tim
2657 > 2005-07-13 11:54  tim
2658  
2659          * src/: UseTheForce/fSwitchingFunction.h,
2660          UseTheForce/mpiComponentPlan.h,
# Line 2493 | Line 2666
2666          utils/simError.c, utils/simError.h: replace c++ style comment in c
2667          files
2668  
2669 < 2005-07-03 15:53  chuckv
2669 > 2005-07-03 16:53  chuckv
2670  
2671          * src/: UseTheForce/doForces.F90, UseTheForce/notifyCutoffs.F90,
2672          UseTheForce/DarkSide/simulation.F90, utils/oopseMPI.F90: Added
# Line 2501 | Line 2674
2674          simulation.F90 to determine if a particular atype is present in a
2675          simulation.
2676  
2677 < 2005-06-28 08:58  gezelter
2677 > 2005-06-28 09:58  gezelter
2678  
2679          * src/UseTheForce/doForces.F90: [no log message]
2680  
2681 < 2005-06-27 17:21  chuckv
2681 > 2005-06-27 18:21  chuckv
2682  
2683          * src/UseTheForce/doForces.F90: More breaking and destruction of
2684          force code. Does not build at this point...
2685  
2686 < 2005-06-27 16:01  gezelter
2686 > 2005-06-27 17:01  gezelter
2687  
2688          * src/: UseTheForce/doForces.F90, UseTheForce/DarkSide/atype.F90,
2689          UseTheForce/DarkSide/fInteractionMap.h,
2690          UseTheForce/DarkSide/interactions.F90, utils/definitions.F90:
2691          Breaky breaky!
2692  
2693 < 2005-06-20 11:03  gezelter
2693 > 2005-06-20 12:03  gezelter
2694  
2695          * samples/water/ssd/ssd.md,
2696          src/applications/staticProps/DensityPlot.cpp: fixed a bug and ran a
2697          simulation
2698  
2699 < 2005-06-13 13:25  tim
2699 > 2005-06-13 14:25  tim
2700  
2701          * src/: applications/staticProps/DensityPlot.cpp,
2702          applications/staticProps/DensityPlot.hpp,
# Line 2531 | Line 2704
2704          applications/staticProps/StaticProps.cpp,
2705          io/AtomTypesSectionParser.cpp: working version of DensityPlot
2706  
2707 < 2005-05-31 17:31  chuckv
2707 > 2005-05-31 18:31  chuckv
2708  
2709          * src/: brains/SimInfo.cpp, integrators/Velocitizer.cpp: Changes to
2710          remove angular momentum.
2711  
2712 < 2005-05-31 12:34  chuckv
2712 > 2005-05-31 13:34  chuckv
2713  
2714          * src/applications/nanoRodBuilder/nanorodBuilder.cpp: Fixed bug in
2715          typo in nanorodBuilder.
2716  
2717 < 2005-05-30 09:01  chuckv
2717 > 2005-05-30 10:01  chuckv
2718  
2719          * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
2720          brains/SimInfo.cpp, brains/SimInfo.hpp, brains/Stats.cpp,
# Line 2550 | Line 2723
2723          momentum to velocitizer and added method to calculate system
2724          angular momentum to siminfo.
2725  
2726 < 2005-05-29 16:16  chrisfen
2726 > 2005-05-29 17:16  chrisfen
2727  
2728          * src/UseTheForce/DarkSide/: electrostatic.F90, sticky.F90: Removed
2729          balance from the Darkside (files)
2730  
2731 < 2005-05-29 16:15  chrisfen
2731 > 2005-05-29 17:15  chrisfen
2732  
2733          * src/UseTheForce/doForces.F90: Removed balance from doForces
2734  
2735 < 2005-05-29 16:15  chrisfen
2735 > 2005-05-29 17:15  chrisfen
2736  
2737          * samples/water/tap/: tap.in, tap.md: Updated tap sample
2738  
2739 < 2005-05-29 16:15  chrisfen
2739 > 2005-05-29 17:15  chrisfen
2740  
2741          * samples/water/dimer/: Makefile, tap.in, tap.md: Included a tap
2742          dimer for testing purposes
2743  
2744 < 2005-05-29 16:14  chrisfen
2744 > 2005-05-29 17:14  chrisfen
2745  
2746          * forceFields/DUFF2.frc: Re-entered the TIP4P-Ew water model. It
2747          was apparently wiped earlier this month...
2748  
2749 < 2005-05-29 16:13  chrisfen
2749 > 2005-05-29 17:13  chrisfen
2750  
2751          * ChangeLog: ran make cvslog
2752  
2753 < 2005-05-28 19:16  tim
2753 > 2005-05-28 20:16  tim
2754  
2755          * src/visitors/: AtomNameVisitor.cpp, AtomNameVisitor.hpp: adding
2756          AtomNameVisitor
2757  
2758 < 2005-05-28 19:09  tim
2758 > 2005-05-28 20:09  tim
2759  
2760          * src/integrators/Integrator.cpp: dding resetIntegrator
2761  
2762 < 2005-05-28 19:06  tim
2762 > 2005-05-28 20:06  tim
2763  
2764          * src/integrators/: Integrator.cpp, Integrator.hpp, NPT.cpp,
2765          NPT.hpp, NPTi.cpp, NPTi.hpp, NVT.cpp, NVT.hpp,
2766          VelocityVerletIntegrator.cpp, VelocityVerletIntegrator.hpp: adding
2767          resetIntegrator
2768  
2769 < 2005-05-27 16:11  tim
2769 > 2005-05-27 17:11  tim
2770  
2771          * src/applications/staticProps/: DensityPlot.cpp, DensityPlot.hpp,
2772          Makefile, P2OrderParameter.cpp, SCDOrderParameter.cpp,
# Line 2601 | Line 2774
2774          StaticPropsCmd.c, StaticPropsCmd.h: adding DensityPlot into
2775          StaticProps
2776  
2777 < 2005-05-26 23:41  tim
2777 > 2005-05-27 00:41  tim
2778  
2779          * src/: applications/staticProps/Makefile,
2780          applications/staticProps/P2OrderParameter.cpp,
# Line 2612 | Line 2785
2785          applications/staticProps/StaticPropsCmd.h, utils/StringUtils.cpp,
2786          utils/StringUtils.hpp: adding SCDOrderParameter into StaticProps
2787  
2788 < 2005-05-26 17:45  tim
2788 > 2005-05-26 18:45  tim
2789  
2790          * src/: applications/dump2Xyz/Dump2XYZ.cpp,
2791          applications/dump2Xyz/Dump2XYZCmd.c,
# Line 2632 | Line 2805
2805          wrappingvisitor now wrap back to the center of the mass; adding
2806          P2OrderParameter into StaticProps
2807  
2808 < 2005-05-22 16:36  chuckv
2808 > 2005-05-22 17:36  chuckv
2809  
2810          * src/: applications/nanoRodBuilder/Geometry.cpp,
2811          applications/nanoRodBuilder/GeometryBuilder.cpp,
# Line 2642 | Line 2815
2815          integrators/VelocityVerletIntegrator.cpp: Fix to print pressure
2816          tensor.
2817  
2818 < 2005-05-22 16:05  tim
2818 > 2005-05-22 17:05  tim
2819  
2820          * src/: brains/Stats.cpp, brains/Stats.hpp, brains/Thermo.cpp,
2821          integrators/VelocityVerletIntegrator.cpp, io/Globals.cpp,
2822          io/Globals.hpp, io/SectionParserManager.cpp: adding keyword
2823          printPressureTensor
2824  
2825 < 2005-05-20 14:27  tim
2825 > 2005-05-20 15:27  tim
2826  
2827          * src/integrators/NPrT.cpp: NPrT in progress
2828  
2829 < 2005-05-20 11:01  tim
2829 > 2005-05-20 12:01  tim
2830  
2831          * src/: integrators/NPrT.cpp, io/Globals.cpp,
2832          utils/OOPSEConstant.hpp: NPrT in progress
2833  
2834 < 2005-05-19 16:31  tim
2834 > 2005-05-19 17:31  tim
2835  
2836          * src/: brains/Thermo.cpp, brains/Thermo.hpp, integrators/NPAT.cpp,
2837          integrators/NPrT.cpp, integrators/NPrT.hpp, io/Globals.cpp,
2838          io/Globals.hpp: NPAT is working
2839  
2840 < 2005-05-19 10:49  tim
2840 > 2005-05-19 11:49  tim
2841  
2842          * src/: UseTheForce/DarkSide/LJ.F90, integrators/Makefile,
2843          integrators/NPrT.cpp, io/Globals.cpp: fix bug in NPAT and NPrT
2844  
2845 < 2005-05-18 23:28  tim
2845 > 2005-05-19 00:28  tim
2846  
2847          * src/: brains/Register.cpp, integrators/NPAT.cpp,
2848          integrators/NPAT.hpp, integrators/NPrT.cpp, integrators/NPrT.hpp,
2849          io/Globals.cpp, io/Globals.hpp: adding NPAT and NPrT integrators
2850  
2851 < 2005-05-18 14:06  chrisfen
2851 > 2005-05-18 15:06  chrisfen
2852  
2853          * forceFields/DUFF2.frc, src/UseTheForce/DarkSide/sticky.F90: just
2854          some tap changes
2855  
2856 < 2005-05-18 13:31  chrisfen
2856 > 2005-05-18 14:31  chrisfen
2857  
2858          * src/UseTheForce/: doForces.F90, DarkSide/electrostatic.F90,
2859          DarkSide/sticky.F90: Modifications to temper the dipolar strength
2860          in the first solvation shell for tap
2861  
2862 < 2005-05-18 07:35  chrisfen
2862 > 2005-05-18 08:35  chrisfen
2863  
2864          * samples/water/tap/: tap.in, tap.md, water.md: added a tap example
2865          for testing purposes
2866  
2867 < 2005-05-17 17:35  chrisfen
2867 > 2005-05-17 18:35  chrisfen
2868  
2869          * ChangeLog, forceFields/DUFF2.frc, samples/water/dimer/ssd.md,
2870          samples/water/dimer/water.md, src/UseTheForce/DUFF.cpp,
# Line 2701 | Line 2874
2874          src/UseTheForce/DarkSide/sticky.F90: Modifications to tap.  Also
2875          correcting changes to the previous merge that were not caught
2876  
2877 < 2005-05-16 23:20  chuckv
2877 > 2005-05-17 00:20  chuckv
2878  
2879          * src/types/: DirectionalAtomType.cpp, DirectionalAtomType.hpp:
2880          Fixed merge issues between Kyle and Chris so OOPSE will actually
2881          build.
2882  
2883 < 2005-05-16 22:46  kdaily
2883 > 2005-05-16 23:46  kdaily
2884  
2885          * src/io/: GayBerneAtomTypesSectionParser.cpp,
2886          GayBerneAtomTypesSectionParser.hpp, Makefile: help
2887  
2888 < 2005-05-16 21:08  kdaily
2888 > 2005-05-16 22:08  kdaily
2889  
2890          * forceFields/DUFF2.frc, src/UseTheForce/doForces.F90,
2891          src/UseTheForce/DarkSide/gb.F90, src/io/Makefile,
2892          src/types/DirectionalAtomType.cpp,
2893          src/types/DirectionalAtomType.hpp: added gb
2894  
2895 < 2005-05-13 15:36  chrisfen
2895 > 2005-05-13 16:36  chrisfen
2896  
2897          * forceFields/DUFF2.frc: Better tap
2898  
2899 < 2005-05-12 14:43  chrisfen
2899 > 2005-05-12 15:43  chrisfen
2900  
2901          * forceFields/DUFF2.frc, samples/water/dimer/ssd.in,
2902          samples/water/dimer/ssd.md, src/UseTheForce/DarkSide/sticky.F90,
# Line 2731 | Line 2904
2904          src/visitors/AtomVisitor.hpp: Couple of changes for TAP water.
2905          Need to parametrize.
2906  
2907 < 2005-05-11 18:15  chuckv
2907 > 2005-05-11 19:15  chuckv
2908  
2909          * src/: io/ShapeAtomTypesSectionParser.cpp,
2910          math/RealSphericalHarmonic.cpp, utils/CaseConversion.hpp: Fixed
2911          build issues under ifc7.
2912  
2913 < 2005-05-09 17:07  chuckv
2913 > 2005-05-09 18:07  chuckv
2914  
2915          * src/applications/nanoRodBuilder/Geometry.hpp: More geometry
2916          builder changes.
2917  
2918 < 2005-05-05 10:06  chrisfen
2918 > 2005-05-05 11:06  chrisfen
2919  
2920          * forceFields/DUFF2.frc, samples/water/ssde/water.md: Changed SHED
2921          to TAP
2922  
2923 < 2005-05-05 09:47  chrisfen
2923 > 2005-05-05 10:47  chrisfen
2924  
2925          * forceFields/DUFF2.frc, samples/water/ssde/ssde.md,
2926          samples/water/ssde/water.md, src/UseTheForce/DUFF.cpp,
# Line 2765 | Line 2938
2938          src/types/DirectionalAtomType.hpp: OOPSE setup for TAP water.  It's
2939          not parametrized, but OOPSE will now let me run it...
2940  
2941 < 2005-05-03 17:55  chuckv
2941 > 2005-05-03 18:55  chuckv
2942  
2943          * src/applications/nanoRodBuilder/: Geometry.cpp, Geometry.hpp,
2944          GeometryCreator.hpp, GeometryFactory.cpp, GeometryFactory.hpp:
2945          Adding support for generic geometry to nanorodbuilder.
2946  
2947 < 2005-05-03 12:55  chuckv
2947 > 2005-05-03 13:55  chuckv
2948  
2949          * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
2950          nanorodBuilder.cpp, nanorodBuilder.ggo, nanorodBuilderCmd.c,
2951          nanorodBuilderCmd.h: More changes to nanoRodBuilder....
2952  
2953 < 2005-04-29 14:16  gezelter
2953 > 2005-04-29 15:16  gezelter
2954  
2955          * make/Makefile.in: [no log message]
2956  
2957 < 2005-04-29 11:26  chrisfen
2957 > 2005-04-29 12:26  chrisfen
2958  
2959          * forceFields/DUFF2.frc, samples/water/spce/water.md,
2960          samples/water/ssd/water.md, samples/water/ssd-ion/ssdCl.md,
# Line 2789 | Line 2962
2962          samples/water/ssdrf/water.md, samples/water/tip3p_ice/water.md,
2963          samples/water/tip4p/water.md: Added TIP4P-Ew
2964  
2965 < 2005-04-27 19:24  chuckv
2965 > 2005-04-27 20:24  chuckv
2966  
2967          * src/applications/nanoRodBuilder/: GeometryBuilder.cpp,
2968          GeometryBuilder.hpp, nanorodBuilder.cpp, nanorodBuilder.ggo,
2969          nanorodBuilderCmd.c, nanorodBuilderCmd.h: Fixed issues with
2970          nanoRodBuilder....
2971  
2972 < 2005-04-27 15:13  chrisfen
2972 > 2005-04-27 16:13  chrisfen
2973  
2974          * samples/shape/Shapes.frc, samples/shape/linear.shape,
2975          src/UseTheForce/DarkSide/atype.F90,
# Line 2805 | Line 2978
2978          src/types/AtomType.cpp, src/types/ShapeAtomType.cpp: Got rid of
2979          write statements and am closer to a working shapes
2980  
2981 < 2005-04-22 16:57  chuckv
2981 > 2005-04-22 17:57  chuckv
2982  
2983          * src/utils/Predicate.hpp: Fixed gcc4 bug...
2984  
2985 < 2005-04-22 16:52  tim
2985 > 2005-04-22 17:52  tim
2986  
2987          * src/utils/: CaseConversion.hpp, Predicate.hpp, Trim.cpp,
2988          Trim.hpp: adding CharClassificationFunctor to fix the locale
2989          problem  of c++
2990  
2991 < 2005-04-21 09:12  chrisfen
2991 > 2005-04-21 10:12  chrisfen
2992  
2993          * samples/shape/Shapes.frc, samples/shape/linear.in,
2994          samples/shape/linear.md, src/UseTheForce/ForceField.hpp,
# Line 2835 | Line 3008
3008          bounds overwrite (I think...). At least the parser loads the
3009          forcefield fine...
3010  
3011 < 2005-04-18 10:44  chrisfen
3011 > 2005-04-18 11:44  chrisfen
3012  
3013          * src/UseTheForce/Shapes_FF.cpp: axed because file causes havoc on
3014          Mac (capitalization confusion of filenames)
3015  
3016 < 2005-04-17 22:50  chrisfen
3016 > 2005-04-17 23:50  chrisfen
3017  
3018          * src/: UseTheForce/SHAPES_FF.cpp, UseTheForce/SHAPES_FF.hpp,
3019          UseTheForce/Shapes_FF.cpp,
# Line 2848 | Line 3021
3021          io/ShapeAtomTypesSectionParser.cpp,
3022          io/ShapeAtomTypesSectionParser.hpp: Working on the shapes parser...
3023  
3024 < 2005-04-15 17:43  gezelter
3024 > 2005-04-15 18:43  gezelter
3025  
3026          * README: gmake in case people forget
3027  
3028 < 2005-04-15 17:40  gezelter
3028 > 2005-04-15 18:40  gezelter
3029  
3030          * src/applications/oopse/oopse.cpp: fixed the spacing on the
3031          banner.  Vanity.
3032  
3033 < 2005-04-15 17:22  gezelter
3033 > 2005-04-15 18:22  gezelter
3034  
3035          * src/: config.h.in, applications/oopse/oopse.cpp: Version string
3036          in banner (and version numbers in config.h)
3037  
3038 < 2005-04-15 17:22  gezelter
3038 > 2005-04-15 18:22  gezelter
3039  
3040          * ChangeLog, LICENSE, README: Documentation changes
3041  
3042 < 2005-04-15 17:03  gezelter
3042 > 2005-04-15 18:03  gezelter
3043  
3044          * src/: UseTheForce/DUFF.cpp, UseTheForce/DUFF.hpp,
3045          UseTheForce/EAM_FF.cpp, UseTheForce/EAM_FF.hpp,
# Line 3087 | Line 3260
3260          visitors/ZconsVisitor.cpp, visitors/ZconsVisitor.hpp: xemacs has
3261          been drafted to perform our indentation services
3262  
3263 < 2005-04-15 17:03  gezelter
3263 > 2005-04-15 18:03  gezelter
3264  
3265          * configure, ac-tools/configure.in: Jedi mind-trick warning
3266          messages have been added to make users ignore CGAL.
3267  
3268 < 2005-04-15 13:41  tim
3268 > 2005-04-15 14:41  tim
3269  
3270          * make/Makefile.in: fix make install
3271  
3272 < 2005-04-15 13:41  tim
3272 > 2005-04-15 14:41  tim
3273  
3274          * samples/: dipole/Makefile, shape/Makefile, water/dimer/Makefile:
3275          add  Makefile of samples
3276  
3277 < 2005-04-15 13:33  tim
3277 > 2005-04-15 14:33  tim
3278  
3279          * samples/: lipid/Makefile, water/dimer/Makefile,
3280          water/ssd-ion/Makefile, water/ssdrf/Makefile: some samples are not
3281          installed correctly
3282  
3283 < 2005-04-14 16:41  gezelter
3283 > 2005-04-14 17:41  gezelter
3284  
3285          * ChangeLog, configure, ac-tools/aclocal.m4, ac-tools/configure.in,
3286          make/Makefile.in, scripts/cvs2cl, scripts/cvs2cl.pl,
3287          scripts/filepp, scripts/filepp.in: configure now searches for perl
3288          to use with filepp
3289  
3290 < 2005-04-14 16:20  gezelter
3290 > 2005-04-14 17:20  gezelter
3291  
3292          * src/utils/MoLocator.cpp: Fixed a bug in RigidBodyStamp section of
3293          MoLocator
3294  
3295 < 2005-04-14 14:12  gezelter
3295 > 2005-04-14 15:12  gezelter
3296  
3297          * LICENSE: [no log message]
3298  
3299 < 2005-04-14 11:10  chuckv
3299 > 2005-04-14 12:10  chuckv
3300  
3301          * src/applications/nanoRodBuilder/nanorodBuilder.cpp:
3302          nanorodbuilder now exit's when libCGAL is not present.
3303  
3304 < 2005-04-14 10:20  tim
3304 > 2005-04-14 11:20  tim
3305  
3306          * src/io/make_nodes.h: fix one more warning message in make_nodes
3307  
3308 < 2005-04-13 18:36  chuckv
3308 > 2005-04-13 19:36  chuckv
3309  
3310          * src/UseTheForce/DarkSide/electrostatic_interface.F90: Changed
3311          interface name for SGI Compiler
3312  
3313 < 2005-04-13 18:29  chrisfen
3313 > 2005-04-13 19:29  chrisfen
3314  
3315          * samples/water/ssde/ssde.md: oops...  bad sample
3316  
3317 < 2005-04-13 18:00  chuckv
3317 > 2005-04-13 19:00  chuckv
3318  
3319          * src/config.h.in: Change typo in CGAL.
3320  
3321 < 2005-04-13 17:43  tim
3321 > 2005-04-13 18:43  tim
3322  
3323          * src/: brains/SnapshotManager.hpp, primitives/Torsion.hpp,
3324          selection/SelectionCompiler.hpp: fix some warning messages
3325  
3326 < 2005-04-13 17:30  gezelter
3326 > 2005-04-13 18:30  gezelter
3327  
3328          * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
3329          make/Makefile.in, src/config.h.in,
# Line 3159 | Line 3332
3332          src/applications/nanoRodBuilder/nanorodBuilder.cpp: added CGAL
3333          checks
3334  
3335 < 2005-04-13 15:36  chuckv
3335 > 2005-04-13 16:36  chuckv
3336  
3337          * src/UseTheForce/: DUFF.cpp, DUFF.hpp, Shapes_FF.cpp,
3338          DarkSide/LJ.F90, DarkSide/electrostatic.F90,
# Line 3169 | Line 3342
3342          DarkSide/sticky_interface.F90, DarkSide/sticky_interface.h: Added
3343          destroy methods for Fortran modules.
3344  
3345 < 2005-04-13 15:17  chuckv
3345 > 2005-04-13 16:17  chuckv
3346  
3347          * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.F90,
3348          shapes_interface.h: Added destroy method to clean up memory
3349  
3350 < 2005-04-13 13:41  tim
3350 > 2005-04-13 14:41  tim
3351  
3352          * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
3353          brains/SimCreator.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp,
# Line 3183 | Line 3356
3356          types/MakeStamps.hpp, utils/MoLocator.cpp: more memory leak are
3357          fixed
3358  
3359 < 2005-04-12 17:44  chuckv
3359 > 2005-04-12 18:44  chuckv
3360  
3361          * src/applications/nanoRodBuilder/nanoBuilder.ggo: File not needed
3362          for nanoRodBuilder.
3363  
3364 < 2005-04-12 17:42  tim
3364 > 2005-04-12 18:42  tim
3365  
3366          * src/applications/: nanoRodBuilder/nanorodBuilder.cpp,
3367          simpleBuilder/simpleBuilder.cpp: fix memory leak in nanorodBuilder
3368          and simpleBuilder(forget to delete lattice)
3369  
3370 < 2005-04-12 17:33  tim
3370 > 2005-04-12 18:33  tim
3371  
3372          * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
3373          applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp:
3374          refactory lattice
3375  
3376 < 2005-04-12 17:07  tim
3376 > 2005-04-12 18:07  tim
3377  
3378          * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, CubicLattice.cpp,
3379          CubicLattice.hpp, FCCLattice.cpp, FCCLattice.hpp, Lattice.cpp,
3380          Lattice.hpp, Makefile, FCCLattice.hpp, Lattice.hpp: refactory
3381          LatticeFactory and LatticeCreator
3382  
3383 < 2005-04-12 16:58  tim
3383 > 2005-04-12 17:58  tim
3384  
3385          * src/: applications/nanoRodBuilder/nanorodBuilder.cpp,
3386          applications/simpleBuilder/simpleBuilder.cpp, brains/Register.cpp,
# Line 3216 | Line 3389
3389          lattice/LatticeFactory.cpp, lattice/LatticeFactory.hpp,
3390          lattice/Makefile: refactory LatticeFactory and LatticeCreator
3391  
3392 < 2005-04-12 16:28  gezelter
3392 > 2005-04-12 17:28  gezelter
3393  
3394          * src/utils/: Makefile.in, MoLocator.cpp, MoLocator.hpp,
3395          vector_class.F90: cleaned up vector_class memory leak fix by
3396          deallocating in reverse order of how we allocated.  Also migrated
3397          MoLocator into utils directory
3398  
3399 < 2005-04-12 16:27  gezelter
3399 > 2005-04-12 17:27  gezelter
3400  
3401          * src/lattice/: BaseLattice.cpp, BaseLattice.hpp, Lattice.cpp,
3402          Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp,
3403          LatticeFactory.cpp, LatticeFactory.hpp, Makefile: added lattice
3404          directory
3405  
3406 < 2005-04-12 16:27  gezelter
3406 > 2005-04-12 17:27  gezelter
3407  
3408          * src/applications/: nanoRodBuilder/BaseLattice.cpp,
3409          nanoRodBuilder/BaseLattice.hpp, nanoRodBuilder/Lattice.cpp,
# Line 3248 | Line 3421
3421          simpleBuilder/simpleBuilder.cpp: added lattice directory, so all of
3422          these files are now redundant
3423  
3424 < 2005-04-12 16:27  gezelter
3424 > 2005-04-12 17:27  gezelter
3425  
3426          * src/UseTheForce/DarkSide/: atype_interface.F90,
3427          atype_interface.h: cleaned up memory leak fix
3428  
3429 < 2005-04-12 16:26  gezelter
3429 > 2005-04-12 17:26  gezelter
3430  
3431          * make/Makefile.in: added lattice subdirectory
3432  
3433 < 2005-04-12 15:57  chrisfen
3433 > 2005-04-12 16:57  chrisfen
3434  
3435          * src/UseTheForce/Shapes_FF.cpp: no real changes here, maybe added
3436          a space by accident
3437  
3438 < 2005-04-12 15:56  chrisfen
3438 > 2005-04-12 16:56  chrisfen
3439  
3440          * samples/water/ssd-ion/: ssdCl.in, ssdCl.md, water.md: added
3441          quadrupole sample
3442  
3443 < 2005-04-12 15:56  chrisfen
3443 > 2005-04-12 16:56  chrisfen
3444  
3445          * samples/water/dimer/: cl.in, cl.md, cl2.in, cl2.md: updating
3446          samples
3447  
3448 < 2005-04-12 13:30  tim
3448 > 2005-04-12 14:30  tim
3449  
3450          * src/UseTheForce/: ForceField.cpp, ForceField.hpp: destory atom
3451          type in fortran side
3452  
3453 < 2005-04-12 12:45  chuckv
3453 > 2005-04-12 13:45  chuckv
3454  
3455          * src/utils/vector_class.F90: Further changes to vector_class
3456          destroy function.
3457  
3458 < 2005-04-12 12:39  chuckv
3458 > 2005-04-12 13:39  chuckv
3459  
3460          * src/utils/vector_class.F90: Fixed pointer memory leak in
3461          vector_class.
3462  
3463 < 2005-04-12 12:12  chuckv
3463 > 2005-04-12 13:12  chuckv
3464  
3465          * src/UseTheForce/: EAM_FF.cpp, EAM_FF.hpp,
3466          DarkSide/atype_interface.F90, DarkSide/atype_interface.h,
3467          DarkSide/eam.F90, DarkSide/eam_interface.F90,
3468          DarkSide/eam_interface.h: Updates to deallocate object in fortran.
3469  
3470 < 2005-04-12 09:24  chrisfen
3470 > 2005-04-12 10:24  chrisfen
3471  
3472          * src/integrators/VelocityVerletIntegrator.cpp: minor change to TI
3473          output
3474  
3475 < 2005-04-11 19:29  chuckv
3475 > 2005-04-11 20:29  chuckv
3476  
3477          * src/: UseTheForce/DarkSide/atype.F90,
3478          applications/nanoRodBuilder/Makefile: Changes to delete atypes...
3479  
3480 < 2005-04-11 19:28  chuckv
3480 > 2005-04-11 20:28  chuckv
3481  
3482          * src/utils/vector_class.F90: Added code to delete vector.
3483  
3484 < 2005-04-11 16:58  tim
3484 > 2005-04-11 17:58  tim
3485  
3486          * src/io/basic_ifstrstream.hpp: avoid multiple inherit in
3487          basic_ifstrstream
3488  
3489 < 2005-04-11 16:37  chuckv
3489 > 2005-04-11 17:37  chuckv
3490  
3491          * make/Makefile.in,
3492          src/applications/nanoRodBuilder/BaseLattice.cpp,
# Line 3337 | Line 3510
3510          nanoRodBuilder application (may not work yet).  ((Doesn't work
3511          yet.)) (((May never work....)))
3512  
3513 < 2005-04-11 15:54  tim
3513 > 2005-04-11 16:54  tim
3514  
3515          * src/applications/dump2Xyz/Dump2XYZ.cpp: forget to delete
3516          prepareVisitor in Dump2XYZ
3517  
3518 < 2005-04-11 15:19  chrisfen
3518 > 2005-04-11 16:19  chrisfen
3519  
3520          * src/UseTheForce/DarkSide/electrostatic.F90: fixing of the
3521          quadrupoles.  look!  it's divide by 3 like stone says!
3522  
3523 < 2005-04-11 15:18  chrisfen
3523 > 2005-04-11 16:18  chrisfen
3524  
3525          * forceFields/DUFF2.frc: fixing of the quadrupoles
3526  
3527 < 2005-04-11 15:16  tim
3527 > 2005-04-11 16:16  tim
3528  
3529          * src/selection/Token.hpp: change the parameter name in
3530          constructors
3531  
3532 < 2005-04-11 14:49  gezelter
3532 > 2005-04-11 15:49  gezelter
3533  
3534          * make/Makefile.in: One more bug fix for GNU make versions < 3.80
3535  
3536 < 2005-04-11 14:06  gezelter
3536 > 2005-04-11 15:06  gezelter
3537  
3538          * make/Makefile.in: Fixed the uc and lc functions for GNU make
3539          versions < 3.80
3540  
3541 < 2005-04-11 11:13  gezelter
3541 > 2005-04-11 12:13  gezelter
3542  
3543          * make/Makefile.in, src/UseTheForce/Makefile,
3544          src/UseTheForce/DarkSide/Makefile, src/utils/Makefile.in: added
3545          some stuff to clean out module files during "make clean"
3546  
3547 < 2005-04-08 17:13  chrisfen
3547 > 2005-04-08 18:13  chrisfen
3548  
3549          * src/UseTheForce/DarkSide/electrostatic.F90: quadrupole
3550          interactions should be working with a remaining question of
3551          interaction magnitude
3552  
3553 < 2005-04-08 17:12  chrisfen
3553 > 2005-04-08 18:12  chrisfen
3554  
3555          * samples/water/dimer/: cl.in, cl.md, ssd.in, ssd.md: messing with
3556          samples
3557  
3558 < 2005-04-08 13:48  chrisfen
3558 > 2005-04-08 14:48  chrisfen
3559  
3560          * samples/water/ssd/ssd.md: oops...  messed up a sample
3561  
3562 < 2005-04-08 09:43  chrisfen
3562 > 2005-04-08 10:43  chrisfen
3563  
3564          * src/UseTheForce/DarkSide/electrostatic.F90: Altered signs to fix
3565          charge-dipole interactions
3566  
3567 < 2005-04-08 09:42  chrisfen
3567 > 2005-04-08 10:42  chrisfen
3568  
3569          * samples/water/: dimer/cl.in, dimer/cl.md, dimer/water.md,
3570          ssd/ssd.md, ssd/water.md: changes during debug of charge-dipole
3571  
3572 < 2005-04-08 09:41  chrisfen
3572 > 2005-04-08 10:41  chrisfen
3573  
3574          * forceFields/DUFF2.frc: added Cl- and Na+
3575  
3576 < 2005-04-06 18:59  tim
3576 > 2005-04-06 19:59  tim
3577  
3578          * src/io/BASSlex.l: reinitialize buffer_stack_ptr in BASS parser
3579  
3580 < 2005-04-05 18:09  tim
3580 > 2005-04-05 19:09  tim
3581  
3582          * src/selection/: NameFinder.cpp, SelectionCompiler.cpp,
3583          SelectionCompiler.hpp, Token.hpp, TokenMap.cpp: support '+' and '-'
# Line 7309 | Line 7482
7482          DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.cpp,
7483          StuntDouble.hpp: these core classes get compiled
7484  
7485 < 2004-10-29 17:37  tim
7485 > 2004-10-29 18:37  tim
7486  
7487          * test/brains/: Molecule.cpp, Molecule.hpp: more work on Molecule
7488          class
7489  
7490 < 2004-10-29 17:28  chrisfen
7490 > 2004-10-29 18:28  chrisfen
7491  
7492          * src/: UseTheForce/DarkSide/atype.F90,
7493          UseTheForce/DarkSide/shapes.F90, math/RealSphericalHarmonic.cpp,
7494          types/ShapeAtomType.cpp: still debugging
7495  
7496 < 2004-10-29 17:28  chrisfen
7496 > 2004-10-29 18:28  chrisfen
7497  
7498          * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, doForces.F90:
7499          shapes rcut calculator added
7500  
7501 < 2004-10-29 17:27  chrisfen
7501 > 2004-10-29 18:27  chrisfen
7502  
7503          * samples/shape/linear.md: shorter run
7504  
7505 < 2004-10-29 15:54  tim
7505 > 2004-10-29 16:54  tim
7506  
7507          * test/brains/: Molecule.cpp, Molecule.hpp: rewrite Molecule class.
7508  
7509 < 2004-10-29 11:22  tim
7509 > 2004-10-29 12:22  tim
7510  
7511          * test/utils/: GenerateCombination.hpp, ReplaceWildCard.hpp,
7512          ReplaceWildCardTestCase.cpp, ReplaceWildCardTestCase.hpp: Remove
7513          some deprecated files
7514  
7515 < 2004-10-29 11:20  tim
7515 > 2004-10-29 12:20  tim
7516  
7517          * test/brains/: Atom.cpp, Atom.hpp, DirectioanlAtom.cpp,
7518          DirectionalAtom.hpp, RigidBody.cpp, RigidBody.hpp, StuntDouble.hpp:
7519          More painful reconstruction is coming !!!
7520  
7521 < 2004-10-28 17:34  tim
7521 > 2004-10-28 18:34  tim
7522  
7523          * src/brains/DataStorage.hpp, src/utils/next_combination.hpp,
7524          test/brains/DirectioanlAtom.cpp, test/brains/DirectionalAtom.hpp,
# Line 7353 | Line 7526
7526          test/brains/StuntDouble.hpp: More work on StuntDouble, Atom,
7527          DirectionalAtom and RigidBody
7528  
7529 < 2004-10-28 17:26  tim
7529 > 2004-10-28 18:26  tim
7530  
7531          * ChangeLog, src/applications/simpleBuilder/BaseLattice.hpp,
7532          src/applications/simpleBuilder/MoLocator.cpp,
# Line 7361 | Line 7534
7534          src/utils/GenericFactory.hpp, src/utils/next_combination.hpp:
7535          remove old Vector3d.hpp from application/simpleBuilder
7536  
7537 < 2004-10-28 16:42  tim
7537 > 2004-10-28 17:42  tim
7538  
7539          * src/utils/next_combination.hpp: Minor change in next_combination
7540  
7541 < 2004-10-28 16:28  tim
7541 > 2004-10-28 17:28  tim
7542  
7543          * src/utils/next_combination.hpp,
7544          test/utils/NextCombinationTestCase.cpp,
7545          test/utils/ReplaceWildCardTestCase.cpp: Done with combination
7546  
7547 < 2004-10-28 16:11  tim
7547 > 2004-10-28 17:11  tim
7548  
7549          * src/utils/next_combination.hpp: change documentation of
7550          next_combination.hpp
7551  
7552 < 2004-10-28 15:41  tim
7552 > 2004-10-28 16:41  tim
7553  
7554          * ChangeLog, src/utils/next_combination.hpp,
7555          test/utils/NextCombinationTestCase.cpp,
7556          test/utils/NextCombinationTestCase.hpp: ReplaceWildCard is working
7557  
7558 < 2004-10-28 15:01  tim
7558 > 2004-10-28 16:01  tim
7559  
7560          * src/utils/next_combination.hpp: adding replace wildcard function
7561  
7562 < 2004-10-28 14:33  tim
7562 > 2004-10-28 15:33  tim
7563  
7564          * src/utils/next_combination.hpp: Minor change
7565  
7566 < 2004-10-28 14:06  tim
7566 > 2004-10-28 15:06  tim
7567  
7568          * ChangeLog, src/applications/simpleBuilder/MoLocator.hpp,
7569          src/applications/simpleBuilder/simpleBuilder.cpp,
# Line 7400 | Line 7573
7573          test/utils/next_combination.hpp: STL next_permutation like
7574          next_combination is working
7575  
7576 < 2004-10-28 12:22  chrisfen
7576 > 2004-10-28 13:22  chrisfen
7577  
7578          * src/UseTheForce/WATER.cpp: fix of setDipoles
7579  
7580 < 2004-10-28 12:20  gezelter
7580 > 2004-10-28 13:20  gezelter
7581  
7582          * src/UseTheForce/Shapes_FF.cpp: forgot to advance lines in the
7583          shapeFile
7584  
7585 < 2004-10-28 12:20  gezelter
7585 > 2004-10-28 13:20  gezelter
7586  
7587          * samples/shape/linear.md: forgot the orientation line
7588  
7589 < 2004-10-28 11:56  gezelter
7589 > 2004-10-28 12:56  gezelter
7590  
7591          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
7592          UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
7593          UseTheForce/WATER.cpp, types/AtomType.cpp: fixed duplicate
7594          declaration foo
7595  
7596 < 2004-10-28 11:55  gezelter
7596 > 2004-10-28 12:55  gezelter
7597  
7598          * samples/lipid/5x5.md: uncommented .in line
7599  
7600 < 2004-10-28 10:42  tim
7600 > 2004-10-28 11:42  tim
7601  
7602          * test/utils/: Makefile, NextCombinationTestCase.cpp,
7603          NextCombinationTestCase.hpp, next_combination.hpp: next_combination
7604          in progress
7605  
7606 < 2004-10-28 10:15  tim
7606 > 2004-10-28 11:15  tim
7607  
7608          * test/utils/: NextCombinationTestCase.cpp,
7609          NextCombinationTestCase.hpp: adding next_combination test case
7610  
7611 < 2004-10-28 10:02  tim
7611 > 2004-10-28 11:02  tim
7612  
7613          * test/utils/next_combination.hpp: STL Compatible combination
7614          sequence generator
7615  
7616 < 2004-10-28 01:23  tim
7616 > 2004-10-28 02:23  tim
7617  
7618          * test/utils/: GenerateCombination.hpp,
7619          ReplaceWildCardTestCase.cpp: bug fixed in GenerateCombination.hpp
7620  
7621 < 2004-10-28 01:16  tim
7621 > 2004-10-28 02:16  tim
7622  
7623          * test/utils/GenerateCombination.hpp: a STL next_permutaion like
7624          next_combination function.
7625  
7626 < 2004-10-27 22:27  tim
7626 > 2004-10-27 23:27  tim
7627  
7628          * test/utils/ReplaceWildCard.hpp: no message
7629  
7630 < 2004-10-27 22:14  tim
7630 > 2004-10-27 23:14  tim
7631  
7632          * test/utils/: ReplaceWildCard.hpp, ReplaceWildCardTestCase.cpp:
7633          ReplaceWildCard(recursive version) is working, need refactoring. An
7634          iterative version is on the way
7635  
7636 < 2004-10-27 21:28  tim
7636 > 2004-10-27 22:28  tim
7637  
7638          * test/utils/: Makefile, ReplaceWildCard.hpp,
7639          ReplaceWildCardTestCase.cpp: ReplaceWildCard in progress
7640  
7641 < 2004-10-27 21:08  tim
7641 > 2004-10-27 22:08  tim
7642  
7643          * test/utils/: ReplaceWildCardTestCase.cpp,
7644          ReplaceWildCardTestCase.hpp: Adding Test Case for ReplaceWildCard
7645  
7646 < 2004-10-27 18:17  tim
7646 > 2004-10-27 19:17  tim
7647  
7648          * test/utils/ReplaceWildCard.hpp: adding ReplaceWildCard.hpp, need
7649          test
7650  
7651 < 2004-10-27 01:25  tim
7651 > 2004-10-27 02:25  tim
7652  
7653          * src/utils/TupleMatcher.hpp: Adding Generic TupleMatcher, wild
7654          char matching is on the way
7655  
7656 < 2004-10-27 01:07  tim
7656 > 2004-10-27 02:07  tim
7657  
7658          * src/utils/Tuple.hpp: Adding Generic Tuple3 and Tuple4
7659  
7660 < 2004-10-26 22:00  gezelter
7660 > 2004-10-26 23:00  gezelter
7661  
7662          * src/UseTheForce/: EAM_FF.cpp, ForceFields.hpp: bug fix
7663  
7664 < 2004-10-26 21:20  gezelter
7664 > 2004-10-26 22:20  gezelter
7665  
7666          * src/UseTheForce/ForceFields.hpp: subclass foo
7667  
7668 < 2004-10-26 21:16  gezelter
7668 > 2004-10-26 22:16  gezelter
7669  
7670          * src/UseTheForce/: EAM_FF.cpp, LJFF.cpp, WATER.cpp: more char* ->
7671          string conversion
7672  
7673 < 2004-10-26 19:01  gezelter
7673 > 2004-10-26 20:01  gezelter
7674  
7675          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
7676          UseTheForce/ForceFields.hpp, brains/SimSetup.cpp,
7677          brains/SimSetup.hpp: char* -> string
7678  
7679 < 2004-10-26 17:25  gezelter
7679 > 2004-10-26 18:25  gezelter
7680  
7681          * src/types/: AtomType.cpp, AtomType.hpp, DirectionalAtomType.hpp,
7682          Makefile, ShapeAtomType.cpp, ShapeAtomType.hpp, ShapeType.cpp,
7683          ShapeType.hpp: Making ShapeType into a ShapeAtomType, fixing some
7684          isXXX
7685  
7686 < 2004-10-26 17:25  gezelter
7686 > 2004-10-26 18:25  gezelter
7687  
7688          * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
7689          define name collision
7690  
7691 < 2004-10-26 17:24  gezelter
7691 > 2004-10-26 18:24  gezelter
7692  
7693          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
7694          UseTheForce/ForceFields.hpp, UseTheForce/LJFF.cpp,
# Line 7524 | Line 7697
7697          UseTheForce/DarkSide/shapes_interface.h, brains/SimSetup.cpp:
7698          forcefield refactoring for shapes
7699  
7700 < 2004-10-26 17:24  gezelter
7700 > 2004-10-26 18:24  gezelter
7701  
7702          * samples/shape/: 5CB.shape, 8CB.shape, C60.shape, C70.shape,
7703          Shapes.frc, cholesterol.shape, ethylBenzene.shape, linear.in,
7704          linear.md, linear.shape, toluene.shape: adding sample shape
7705          directory
7706  
7707 < 2004-10-26 17:19  tim
7707 > 2004-10-26 18:19  tim
7708  
7709          * ChangeLog, src/brains/DataStorage.cpp,
7710          src/brains/DataStorage.hpp, src/brains/Snapshot.hpp,
# Line 7539 | Line 7712
7712          test/brains/DataStorageTestCase.hpp, test/brains/Makefile:
7713          DataStorage passes unit test
7714  
7715 < 2004-10-26 13:03  chrisfen
7715 > 2004-10-26 14:03  chrisfen
7716  
7717          * src/UseTheForce/DarkSide/: shapes.F90, shapes_interface.h:
7718          Changes to help advance shapes
7719  
7720 < 2004-10-26 13:02  chrisfen
7720 > 2004-10-26 14:02  chrisfen
7721  
7722          * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp: Changes to
7723          Shapes force field reader
7724  
7725 < 2004-10-26 12:28  tim
7725 > 2004-10-26 13:28  tim
7726  
7727          * src/brains/Snapshot.hpp, test/brains/RigidBody.hpp: Snaphot and
7728          SnapshotTestCase in progress
7729  
7730 < 2004-10-25 17:46  tim
7730 > 2004-10-25 18:46  tim
7731  
7732          * ChangeLog, src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
7733          src/math/SquareMatrix3.hpp, src/math/Vector.hpp,
# Line 7563 | Line 7736
7736          test/math/VectorTestCase.cpp: add getArray function to  RectMatrix
7737          and Vector classes
7738  
7739 < 2004-10-25 12:03  tim
7739 > 2004-10-25 13:03  tim
7740  
7741          * ChangeLog, src/utils/GenericFactory.hpp,
7742          test/utils/GenericFactoryTestCase.cpp,
# Line 7571 | Line 7744
7744          GenericFactory Test Case. GenericFactory now can bed used to creat
7745          ForcefieldFactory and IntegratorFactory etc.
7746  
7747 < 2004-10-24 23:08  tim
7747 > 2004-10-25 00:08  tim
7748  
7749          * src/: brains/SimModel.hpp, brains/SimSnapshotManager.cpp,
7750          brains/SimSnapshotManager.hpp, brains/Snapshot.hpp,
7751          brains/SnapshotManager.hpp, utils/GenericFactory.hpp: more classes
7752          get reconstructed
7753  
7754 < 2004-10-24 02:55  tim
7754 > 2004-10-24 03:55  tim
7755  
7756          * src/utils/GenericFactory.hpp: GenericFactory pass unit test
7757  
7758 < 2004-10-23 18:09  tim
7758 > 2004-10-23 19:09  tim
7759  
7760          * test/brains/: Atom.hpp, DirectionalAtom.hpp, RigidBody.hpp,
7761          StuntDouble.cpp, StuntDouble.hpp, Atom.cpp, DirectioanlAtom.cpp,
7762          RigidBody.cpp: Refactoring in progress
7763  
7764 < 2004-10-22 18:09  tim
7764 > 2004-10-22 19:09  tim
7765  
7766          * ChangeLog, src/brains/Snapshot.hpp,
7767          src/brains/SnapshotManager.hpp, src/math/SquareMatrix.hpp,
7768          test/brains/SnapshotTestCase.cpp, test/brains/SnapshotTestCase.hpp,
7769          test/brains/StuntDouble.hpp: more work in Snapshot
7770  
7771 < 2004-10-22 17:59  chrisfen
7771 > 2004-10-22 18:59  chrisfen
7772  
7773          * src/: UseTheForce/LJFF.cpp,
7774          UseTheForce/DarkSide/atype_interface.h, types/AtomType.cpp: Dear
7775          god!  It runs and conserves energy!
7776  
7777 < 2004-10-22 17:54  chrisfen
7777 > 2004-10-22 18:54  chrisfen
7778  
7779          * src/types/: AtomType.cpp, AtomType.hpp: strDUP not strCOPY
7780  
7781 < 2004-10-22 17:53  chrisfen
7781 > 2004-10-22 18:53  chrisfen
7782  
7783          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
7784          UseTheForce/LJFF.cpp, UseTheForce/Shapes_FF.cpp,
# Line 7613 | Line 7786
7786          brains/SimInfo.cpp, brains/SimInfo.hpp: fixey fixey the breakey
7787          breakey
7788  
7789 < 2004-10-22 17:53  chrisfen
7789 > 2004-10-22 18:53  chrisfen
7790  
7791          * make/Makefile.in: compiler flags
7792  
7793 < 2004-10-22 16:20  gezelter
7793 > 2004-10-22 17:20  gezelter
7794  
7795          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
7796          UseTheForce/LJFF.cpp, UseTheForce/doForces.F90,
7797          brains/fSimulation.h, types/AtomType.hpp,
7798          types/DirectionalAtomType.hpp: fixey fixey
7799  
7800 < 2004-10-22 15:22  gezelter
7800 > 2004-10-22 16:22  gezelter
7801  
7802          * src/UseTheForce/DarkSide/: LJ.F90, atype.F90, atype_interface.h,
7803          charge.F90, charge_interface.h, dipole.F90, dipole_interface.h,
7804          lj_interface.h, shapes.F90, simulation.F90: Added un-busticated
7805          fortran files and c/Fortran interfaces
7806  
7807 < 2004-10-22 15:21  gezelter
7807 > 2004-10-22 16:21  gezelter
7808  
7809          * src/types/: AtomType.cpp, AtomType.hpp, AtomTypeProperties.h,
7810          DirectionalAtomType.hpp, Makefile: More on AtomType and
7811          DirectionalAtomType
7812  
7813 < 2004-10-22 09:47  gezelter
7813 > 2004-10-22 10:47  gezelter
7814  
7815          * src/types/AtomType.hpp: Adding AtomType
7816  
7817 < 2004-10-21 16:31  tim
7817 > 2004-10-21 17:31  tim
7818  
7819          * ChangeLog, src/brains/Snapshot.hpp,
7820          src/brains/SnapshotManager.hpp, src/math/RectMatrix.hpp,
# Line 7650 | Line 7823
7823          test/math/RectMatrixTestCase.cpp, test/math/VectorTestCase.cpp:
7824          Snapshot and SnapshotManager in progress
7825  
7826 < 2004-10-21 16:30  tim
7826 > 2004-10-21 17:30  tim
7827  
7828          * test/brains/: BrainsTest.cpp, Makefile,
7829          SnapshotManagerTestCase.cpp, SnapshotManagerTestCase.hpp,
7830          SnapshotTestCase.cpp, SnapshotTestCase.hpp: adding test case for
7831          Snapshot and snapshotManager.
7832  
7833 < 2004-10-21 15:15  gezelter
7833 > 2004-10-21 16:15  gezelter
7834  
7835          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
7836          UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
# Line 7668 | Line 7841
7841          brains/SimSetup.cpp, types/AtomTypeProperties.h: Breaky Breaky.  
7842          Fixey Fixey.
7843  
7844 < 2004-10-21 11:32  tim
7844 > 2004-10-21 12:32  tim
7845  
7846          * src/utils/GenericData.cpp, src/utils/Makefile,
7847          test/utils/Makefile, test/utils/UtilTest: remove some junk files
7848  
7849 < 2004-10-21 11:24  tim
7849 > 2004-10-21 12:24  tim
7850  
7851          * test/utils/GenericData.hpp: remove backup of  GenericData.hpp
7852  
7853 < 2004-10-21 11:22  tim
7853 > 2004-10-21 12:22  tim
7854  
7855          * ChangeLog, src/brains/SimSetup.cpp,
7856          src/constraints/ZConstraint.cpp, src/constraints/ZconsData.hpp,
# Line 7695 | Line 7868
7868          src/visitors/ZconsVisitor.hpp: replace old GebericData with  new
7869          GenericData
7870  
7871 < 2004-10-21 10:25  chuckv
7871 > 2004-10-21 11:25  chuckv
7872  
7873          * src/UseTheForce/DarkSide/: LJ.F90, eam.F90: Added newLJtype to lj
7874          module.
7875  
7876 < 2004-10-21 10:24  chuckv
7876 > 2004-10-21 11:24  chuckv
7877  
7878          * src/UseTheForce/DarkSide/lj_interface.h: Added interface for
7879          fortran lj module.
7880  
7881 < 2004-10-20 17:54  tim
7881 > 2004-10-20 18:54  tim
7882  
7883          * ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp,
7884          test/utils/GenericDataTestCase.cpp, test/utils/Makefile,
# Line 7713 | Line 7886
7886          test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest:
7887          GenericData and PropertyMap  pass unit test.
7888  
7889 < 2004-10-20 16:52  gezelter
7889 > 2004-10-20 17:52  gezelter
7890  
7891          * src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90,
7892          DarkSide/sticky_interface.h: fixed a fortran name problem
7893  
7894 < 2004-10-20 16:38  tim
7894 > 2004-10-20 17:38  tim
7895  
7896          * test/utils/: GenericData.hpp, GenericDataTestCase.cpp,
7897          GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp,
7898          UtilTest, UtilTest.cpp: adding generic data test case
7899  
7900 < 2004-10-20 16:16  chuckv
7900 > 2004-10-20 17:16  chuckv
7901  
7902          * configure, ac-tools/aclocal.m4,
7903          src/UseTheForce/DarkSide/Makefile,
# Line 7736 | Line 7909
7909          Fortran/C++ interface de-obfuscation project appears to be
7910          complete!  Woo hoo!
7911  
7912 < 2004-10-20 15:47  chuckv
7912 > 2004-10-20 16:47  chuckv
7913  
7914          * src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp,
7915          fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project
7916          continues
7917  
7918 < 2004-10-20 15:46  chuckv
7918 > 2004-10-20 16:46  chuckv
7919  
7920          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
7921          UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
# Line 7759 | Line 7932
7932          brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface
7933          de-obfuscation project (It is a very long story)
7934  
7935 < 2004-10-20 13:07  tim
7935 > 2004-10-20 14:07  tim
7936  
7937          * ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp,
7938          test/math/SquareMatrix3TestCase.cpp,
7939          test/math/SquareMatrixTestCase.cpp,
7940          test/math/SquareMatrixTestCase.hpp: Math library pass the unit test
7941  
7942 < 2004-10-20 00:52  tim
7942 > 2004-10-20 01:52  tim
7943  
7944          * src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and
7945          SnapshotManager in design phase
7946  
7947 < 2004-10-19 23:54  gezelter
7947 > 2004-10-20 00:54  gezelter
7948  
7949          * src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace
7950          problem prevented linking
7951  
7952 < 2004-10-19 23:54  gezelter
7952 > 2004-10-20 00:54  gezelter
7953  
7954          * src/UseTheForce/Shapes_FF.cpp: fixed include
7955  
7956 < 2004-10-19 23:26  gezelter
7956 > 2004-10-20 00:26  gezelter
7957  
7958          * src/utils/: Makefile, definitions.F90, definitions_module.F90,
7959          oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90:
7960          more fortran name mangling
7961  
7962 < 2004-10-19 23:23  gezelter
7962 > 2004-10-20 00:23  gezelter
7963  
7964          * src/profiling/timing.F90: yet more fortran renaming
7965  
7966 < 2004-10-19 23:19  gezelter
7966 > 2004-10-20 00:19  gezelter
7967  
7968          * src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h,
7969          do_Forces.F90, do_Forces.h, notifyCutoffs.F90,
7970          notifyCutoffs_interface.h, notifycutoffs_module_interface.h,
7971          wrappers.F90: Fortran name cleanup continues
7972  
7973 < 2004-10-19 23:12  gezelter
7973 > 2004-10-20 00:12  gezelter
7974  
7975          * src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some
7976          broken fortran stuff
7977  
7978 < 2004-10-19 23:02  gezelter
7978 > 2004-10-20 00:02  gezelter
7979  
7980          * src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90,
7981          atype_interface.h, atype_module.F90, atype_module_interface.h,
# Line 7819 | Line 7992
7992          sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90:
7993          name sanity on the fortran side
7994  
7995 < 2004-10-19 19:18  tim
7995 > 2004-10-19 20:18  tim
7996  
7997          * test/math/SquareMatrix3TestCase.hpp: [no log message]
7998  
7999 < 2004-10-19 18:01  tim
7999 > 2004-10-19 19:01  tim
8000  
8001          * src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
8002          src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp:
8003          except diagonalize(), all of functions in math library pass the
8004          test
8005  
8006 < 2004-10-19 17:43  chuckv
8006 > 2004-10-19 18:43  chuckv
8007  
8008          * src/UseTheForce/do_Forces.h: Added correct prototypes for
8009          C-fortran interface functions.
8010  
8011 < 2004-10-19 17:37  chuckv
8011 > 2004-10-19 18:37  chuckv
8012  
8013          * src/UseTheForce/DarkSide/: atype_module_interface.h,
8014          eam_module_inteface.h, gb_module_interface.h,
# Line 7843 | Line 8016
8016          sticky_pair_module_interface.h: Added correct prototypes for
8017          C-fortran interface functions.
8018  
8019 < 2004-10-19 16:28  tim
8019 > 2004-10-19 17:28  tim
8020  
8021          * ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp,
8022          src/math/SquareMatrix.hpp, src/math/Vector.hpp,
# Line 7853 | Line 8026
8026          test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more
8027          bugs get fixed at math library
8028  
8029 < 2004-10-19 15:43  chuckv
8029 > 2004-10-19 16:43  chuckv
8030  
8031          * src/UseTheForce/: DarkSide/atype_module_interface.h,
8032          DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h,
# Line 7867 | Line 8040
8040          notifycutoffs_module_interface.h: Added new files for fortran
8041          interface.
8042  
8043 < 2004-10-19 15:43  gezelter
8043 > 2004-10-19 16:43  gezelter
8044  
8045          * src/UseTheForce/Makefile: regressing
8046  
8047 < 2004-10-19 15:40  gezelter
8047 > 2004-10-19 16:40  gezelter
8048  
8049          * src/: UseTheForce/DarkSide/calc_shapes.F90,
8050          UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp:
8051          working on shapes for portability
8052  
8053 < 2004-10-19 15:40  gezelter
8053 > 2004-10-19 16:40  gezelter
8054  
8055          * src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes
8056  
8057 < 2004-10-19 13:21  chrisfen
8057 > 2004-10-19 14:21  chrisfen
8058  
8059          * src/utils/: StringUtils.cpp, StringUtils.hpp: changed around
8060          findBegin
8061  
8062 < 2004-10-18 23:34  tim
8062 > 2004-10-19 00:34  tim
8063  
8064          * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs
8065          are fixed in Vector class
8066  
8067 < 2004-10-18 23:28  tim
8067 > 2004-10-19 00:28  tim
8068  
8069          * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix
8070          some bugs in RectMatrixTestCase
8071  
8072 < 2004-10-18 23:21  tim
8072 > 2004-10-19 00:21  tim
8073  
8074          * src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp,
8075          test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp,
8076          test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp,
8077          test/math/VectorTestCase.hpp: implement more test cases
8078  
8079 < 2004-10-18 18:13  tim
8079 > 2004-10-18 19:13  tim
8080  
8081          * ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp,
8082          src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp,
# Line 7912 | Line 8085
8085          test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more
8086          tests on math library
8087  
8088 < 2004-10-18 16:03  tim
8088 > 2004-10-18 17:03  tim
8089  
8090          * test/math/: Makefile, QuaternionTestCase.cpp,
8091          QuaternionTestCase.hpp, RectMatrixTestCase.cpp,
# Line 7920 | Line 8093
8093          Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding
8094          more testing units
8095  
8096 < 2004-10-18 12:07  tim
8096 > 2004-10-18 13:07  tim
8097  
8098          * src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp,
8099          math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp,
8100          math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp,
8101          utils/GenericFactory.hpp: fix some bugs in Quaternion class
8102  
8103 < 2004-10-18 11:30  gezelter
8103 > 2004-10-18 12:30  gezelter
8104  
8105          * src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp:
8106          Your basic run of the mill real-valued versions of Y_l^m(\theta,
8107          \phi)
8108  
8109 < 2004-10-18 11:29  gezelter
8109 > 2004-10-18 12:29  gezelter
8110  
8111          * src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp,
8112          types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp,
8113          utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting
8114          Shapes into OOPSE
8115  
8116 < 2004-10-18 10:21  gezelter
8116 > 2004-10-18 11:21  gezelter
8117  
8118          * src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType
8119  
8120 < 2004-10-18 00:23  tim
8120 > 2004-10-18 01:23  tim
8121  
8122          * test/math/VectorTestCase.hpp: adding  vector test case
8123  
8124 < 2004-10-18 00:23  tim
8124 > 2004-10-18 01:23  tim
8125  
8126          * src/utils/GenericFactory.hpp: adding generic factory and vector
8127          test case
8128  
8129 < 2004-10-16 20:19  tim
8129 > 2004-10-16 21:19  tim
8130  
8131          * src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp,
8132          SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in
8133          progress
8134  
8135 < 2004-10-15 20:31  tim
8135 > 2004-10-15 21:31  tim
8136  
8137          * src/math/Quaternion.hpp: add quaternion class
8138  
8139 < 2004-10-15 16:11  tim
8139 > 2004-10-15 17:11  tim
8140  
8141          * test/io/: DUFF.frc, IfstrstreamTestCase.cpp,
8142          IfstrstreamTestCase.hpp: adding test file
8143  
8144 < 2004-10-15 16:10  tim
8144 > 2004-10-15 17:10  tim
8145  
8146          * src/io/basic_ifstrstream.hpp: fix a bunch of bugs
8147  
8148 < 2004-10-15 15:42  tim
8148 > 2004-10-15 16:42  tim
8149  
8150          * src/io/basic_ifstrstream.hpp: change const_cast to statc_const
8151  
8152 < 2004-10-15 15:35  tim
8152 > 2004-10-15 16:35  tim
8153  
8154          * src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp
8155  
8156 < 2004-10-15 15:34  tim
8156 > 2004-10-15 16:34  tim
8157  
8158          * test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use
8159          namespace oopse
8160  
8161 < 2004-10-15 14:38  chuckv
8161 > 2004-10-15 15:38  chuckv
8162  
8163          * configure, ac-tools/aclocal.m4: Changed optimization flags for
8164          XLF and XLC.
8165  
8166 < 2004-10-15 13:28  tim
8166 > 2004-10-15 14:28  tim
8167  
8168          * test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp:
8169          adding ifstrstream test case
8170  
8171 < 2004-10-15 13:20  tim
8171 > 2004-10-15 14:20  tim
8172  
8173          * src/io/basic_ifstrstream.hpp: fix include
8174  
8175 < 2004-10-15 13:18  tim
8175 > 2004-10-15 14:18  tim
8176  
8177          * src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi
8178  
8179 < 2004-10-15 13:17  tim
8179 > 2004-10-15 14:17  tim
8180  
8181          * test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile
8182  
8183 < 2004-10-15 13:16  tim
8183 > 2004-10-15 14:16  tim
8184  
8185          * test/io/: Makefile, ifstrstreamTestCase.cpp,
8186          ifstrstreamTestCase.hpp: adding test case for ifstrstream
8187  
8188 < 2004-10-15 10:37  tim
8188 > 2004-10-15 11:37  tim
8189  
8190          * test/io/: IOTest.cpp, ifstrstreamTestCase.cpp,
8191          ifstrstreamTestCase.hpp: add ifstrstreamTestCase
8192  
8193 < 2004-10-15 10:20  tim
8193 > 2004-10-15 11:20  tim
8194  
8195          * src/io/basic_ifstrstream.hpp: add checkFilename Option
8196  
8197 < 2004-10-15 10:19  tim
8197 > 2004-10-15 11:19  tim
8198  
8199          * test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp,
8200          SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add
8201          SquareMatrixTestCase class
8202  
8203 < 2004-10-15 02:52  tim
8203 > 2004-10-15 03:52  tim
8204  
8205          * src/io/basic_ifstrstream.hpp: adding basic_ifstrstream
8206  
8207 < 2004-10-14 18:28  tim
8207 > 2004-10-14 19:28  tim
8208  
8209          * src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp,
8210          Vector.hpp: math library in progress
8211  
8212 < 2004-10-14 18:27  tim
8212 > 2004-10-14 19:27  tim
8213  
8214          * src/io/FileReader.hpp: FileReader in progress
8215  
8216 < 2004-10-13 18:53  tim
8216 > 2004-10-13 19:53  tim
8217  
8218          * src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress,
8219          test in isOrthogonal of SquareMatrix is failed by some reasons
8220  
8221 < 2004-10-13 17:28  tim
8221 > 2004-10-13 18:28  tim
8222  
8223          * src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap
8224          class
8225  
8226 < 2004-10-13 17:27  tim
8226 > 2004-10-13 18:27  tim
8227  
8228          * test/math/: MainTest.cpp, RectMatrixTestCase.cpp,
8229          RectMatrixTestCase.hpp: adding testing unit
8230  
8231 < 2004-10-13 17:24  tim
8231 > 2004-10-13 18:24  tim
8232  
8233          * src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix
8234  
8235 < 2004-10-13 01:51  tim
8235 > 2004-10-13 02:51  tim
8236  
8237          * src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp,
8238          Vector3.hpp: refactory vector and matrix classes
8239  
8240 < 2004-10-13 01:50  tim
8240 > 2004-10-13 02:50  tim
8241  
8242          * src/math/Vector3d.hpp: Remove some Makefile.in
8243  
8244 < 2004-10-12 18:57  tim
8244 > 2004-10-12 19:57  tim
8245  
8246          * src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and
8247          Matrix3x3d.hpp
8248  
8249 < 2004-10-12 14:08  tim
8249 > 2004-10-12 15:08  tim
8250  
8251          * doc/: cppstyle.html, style.css: adding c++ coding style
8252  
8253 < 2004-10-11 17:15  tim
8253 > 2004-10-11 18:15  tim
8254  
8255          * src/: constraints/AbstractClasses.hpp,
8256          integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp:
8257          change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp
8258  
8259 < 2004-10-11 16:54  tim
8259 > 2004-10-11 17:54  tim
8260  
8261          * scripts/filepp: fix a bug in filepp
8262  
8263 < 2004-10-11 16:13  tim
8263 > 2004-10-11 17:13  tim
8264  
8265          * make/Makefile.in: using filepp to generate dependencies instead
8266          of compilers
8267  
8268 < 2004-10-11 16:10  tim
8268 > 2004-10-11 17:10  tim
8269  
8270          * scripts/filepp: filepp can be used to generate dependencies for
8271          c/c++ now
8272  
8273 < 2004-10-11 13:40  tim
8273 > 2004-10-11 14:40  tim
8274  
8275          * make/Makefile.in: remove -module from F90Options
8276  
8277 < 2004-10-11 13:01  tim
8277 > 2004-10-11 14:01  tim
8278  
8279          * make/Makefile.in: adding rules to move fortran 90 module to
8280          target directory
8281  
8282 < 2004-10-11 10:43  gezelter
8282 > 2004-10-11 11:43  gezelter
8283  
8284          * make/Makefile.in: fixed makefile.in
8285  
8286 < 2004-10-11 09:51  tim
8286 > 2004-10-11 10:51  tim
8287  
8288          * scripts/filepp: remove "use bytes" which causes problem in sgi
8289          machine
8290  
8291 < 2004-10-11 09:26  tim
8291 > 2004-10-11 10:26  tim
8292  
8293          * forceFields/Makefile: add Makefile
8294  
8295 < 2004-10-11 09:23  tim
8295 > 2004-10-11 10:23  tim
8296  
8297          * samples/: water/dimer/Makefile, water/spce/Makefile,
8298          water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile,
8299          water/tip4p/Makefile, zcons/Makefile: fix Makefile under water
8300          directory
8301  
8302 < 2004-10-11 09:23  tim
8302 > 2004-10-11 10:23  tim
8303  
8304          * samples/argon/Makefile: remove argon.dump and argon.eor from
8305          Makefile
8306  
8307 < 2004-10-09 01:01  tim
8307 > 2004-10-09 02:01  tim
8308  
8309          * samples/: alkane/Makefile.in, argon/Makefile.in,
8310          lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in:
8311          Remove some Makefile.in
8312  
8313 < 2004-10-08 18:15  tim
8313 > 2004-10-08 19:15  tim
8314  
8315          * make/Makefile.in: [no log message]
8316  
8317 < 2004-10-08 17:51  tim
8317 > 2004-10-08 18:51  tim
8318  
8319          * make/Makefile.in: fix make install
8320  
8321 < 2004-10-08 17:10  tim
8321 > 2004-10-08 18:10  tim
8322  
8323          * make/Makefile.in: adding make install
8324  
8325 < 2004-10-08 17:04  tim
8325 > 2004-10-08 18:04  tim
8326  
8327          * samples/: alkane/Makefile, argon/Makefile, lipid/Makefile,
8328          metals/Makefile, minimizer/Makefile, water/Makefile.in,
# Line 8160 | Line 8333
8333          water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile,
8334          zcons/Makefile.in: add Makefile to sample directory
8335  
8336 < 2004-10-06 18:03  gezelter
8336 > 2004-10-06 19:03  gezelter
8337  
8338          * src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt
8339          stuff
8340  
8341 < 2004-10-06 18:03  gezelter
8341 > 2004-10-06 19:03  gezelter
8342  
8343          * configure, ac-tools/aclocal.m4, ac-tools/configure.in,
8344          make/Doxyfile, src/applications/getopt.c,
8345          src/applications/getopt1.c, src/applications/gnugetopt.h: more
8346          build fixes
8347  
8348 < 2004-10-06 17:20  tim
8348 > 2004-10-06 18:20  tim
8349  
8350          * make/: Doxyfile, Makefile.in: adding doxygen configuration file
8351  
8352 < 2004-10-06 17:19  tim
8352 > 2004-10-06 18:19  tim
8353  
8354          * scripts/filepp: filepp can handle different fortran module case
8355          and suffix
8356  
8357 < 2004-10-06 16:27  gezelter
8357 > 2004-10-06 17:27  gezelter
8358  
8359          * src/restraints/Restraints.cpp: Chris doesn't know about the
8360          OOPSE-2.0 directory structure yet
8361  
8362 < 2004-10-06 16:27  gezelter
8362 > 2004-10-06 17:27  gezelter
8363  
8364          * ChangeLog: Yeah yeah, we'lll get around to it later
8365  
8366 < 2004-10-06 16:22  gezelter
8366 > 2004-10-06 17:22  gezelter
8367  
8368          * configure, ac-tools/configure.in, ac-tools/fortran90.m4,
8369          make/Makefile.in: cleaning up build process
8370  
8371 < 2004-10-06 15:01  chrisfen
8371 > 2004-10-06 16:01  chrisfen
8372  
8373          * src/restraints/Restraints.cpp: made the file reading in
8374          restraints more intelligent - no longer gives uninformative seg
8375          faults
8376  
8377 < 2004-10-06 14:55  gezelter
8377 > 2004-10-06 15:55  gezelter
8378  
8379          * src/applications/simpleBuilder/Make.ftemp.old: cleaning up
8380  
8381 < 2004-10-06 14:51  gezelter
8381 > 2004-10-06 15:51  gezelter
8382  
8383          * LICENSE, MPIobj/dummy, make/Makefile, obj/dummy,
8384          scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit
8385  
8386 < 2004-10-06 13:53  tim
8386 > 2004-10-06 14:53  tim
8387  
8388          * make/: Makefile, Makefile.in: fix make statistics
8389  
8390 < 2004-10-06 13:18  tim
8390 > 2004-10-06 14:18  tim
8391  
8392          * make/: Makefile, Makefile.in: adding GNU make functions to
8393          combine all of the static libraries to a big library
8394  
8395 < 2004-10-05 17:57  tim
8395 > 2004-10-05 18:57  tim
8396  
8397          * make/: Makefile, Makefile.in:  adding shared library flag
8398  
8399 < 2004-10-05 14:37  tim
8399 > 2004-10-05 15:37  tim
8400  
8401          * src/: Makefile, UseTheForce/Makefile,
8402          UseTheForce/mpiSimulation_module.F90,
# Line 8231 | Line 8404
8404          UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move
8405          mpiSimulation_module to DarkSide
8406  
8407 < 2004-10-05 14:35  tim
8407 > 2004-10-05 15:35  tim
8408  
8409          * make/: Makefile, Makefile.in: building MPI version;using static
8410          library instead of shared library
8411  
8412 < 2004-10-05 09:14  tim
8412 > 2004-10-05 10:14  tim
8413  
8414          * make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90
8415          to filepp
8416  
8417 < 2004-10-04 15:56  tim
8417 > 2004-10-04 16:56  tim
8418  
8419          * make/: Makefile, Makefile.in: add make cvslog
8420  
8421 < 2004-10-04 11:24  gezelter
8421 > 2004-10-04 12:24  gezelter
8422  
8423          * make/: Makefile, Makefile.in: more work on the parallel build
8424  
8425 < 2004-10-04 11:06  gezelter
8425 > 2004-10-04 12:06  gezelter
8426  
8427          * make/: Makefile, Makefile.in: changes to backport declare flags
8428  
8429 < 2004-10-04 10:27  gezelter
8429 > 2004-10-04 11:27  gezelter
8430  
8431          * src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp,
8432          DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging
8433          shapes
8434  
8435 < 2004-10-01 23:40  tim
8435 > 2004-10-02 00:40  tim
8436  
8437          * scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree
8438  
8439 < 2004-10-01 23:22  tim
8439 > 2004-10-02 00:22  tim
8440  
8441          * make/: Makefile, Makefile.in: add oopse_ as library prefix
8442  
8443 < 2004-10-01 16:59  tim
8443 > 2004-10-01 17:59  tim
8444  
8445          * make/: Makefile, Makefile.in: fix a space trimming bug in filepp
8446  
8447 < 2004-10-01 16:22  gezelter
8447 > 2004-10-01 17:22  gezelter
8448  
8449          * Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A
8450          few minor build changes
8451  
8452 < 2004-10-01 16:11  tim
8452 > 2004-10-01 17:11  tim
8453  
8454          * scripts/filepp: adding fortran90 make dependency tool
8455  
8456 < 2004-09-30 10:41  tim
8456 > 2004-09-30 11:41  tim
8457  
8458          * make/: Makefile, Makefile.in: make clean is smart enough to only
8459          remove object files belong to current package.  turn off silent
8460          mode
8461  
8462 < 2004-09-29 16:55  tim
8462 > 2004-09-29 17:55  tim
8463  
8464          * src/: Makefile, UseTheForce/Makefile,
8465          UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile,
# Line 8297 | Line 8470
8470          restraints/Makefile, types/Makefile, utils/Makefile,
8471          visitors/Makefile: define DEV_ROOT as relative path
8472  
8473 < 2004-09-29 16:54  tim
8473 > 2004-09-29 17:54  tim
8474  
8475          * make/: Makefile, Makefile.in: get the relative path by shell
8476          script
8477  
8478 < 2004-09-29 16:32  tim
8478 > 2004-09-29 17:32  tim
8479  
8480          * make/Makefile: eliminate DEV_ROOT by relative path
8481  
8482 < 2004-09-29 13:37  tim
8482 > 2004-09-29 14:37  tim
8483  
8484          * make/Makefile.in: add PackageLibs;  fix dependency rule
8485  
8486 < 2004-09-29 12:57  gezelter
8486 > 2004-09-29 13:57  gezelter
8487  
8488          * configure, ac-tools/configure.in: updates
8489  
8490 < 2004-09-29 12:56  gezelter
8490 > 2004-09-29 13:56  gezelter
8491  
8492          * make/: Make.conf.in, Makefile.in, _files/style.css: Working on
8493          make stuff
8494  
8495 < 2004-09-29 12:46  tim
8495 > 2004-09-29 13:46  tim
8496  
8497          * Makefile: If makefile does not exist, print error message
8498  
8499 < 2004-09-29 12:12  tim
8499 > 2004-09-29 13:12  tim
8500  
8501          * make/: Make.conf.in, Makefile: fix dependencies rule
8502  
8503 < 2004-09-29 10:58  gezelter
8503 > 2004-09-29 11:58  gezelter
8504  
8505          * Makefile, make/Makefile: still working on build process
8506  
8507 < 2004-09-29 10:00  tim
8507 > 2004-09-29 11:00  tim
8508  
8509          * make/Makefile: add print statment to rules
8510  
8511 < 2004-09-29 09:59  tim
8511 > 2004-09-29 10:59  tim
8512  
8513          * src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile,
8514          applications/dump2Xyz/Makefile, applications/oopse/Makefile,
# Line 8345 | Line 8518
8518          profiling/Makefile, restraints/Makefile, types/Makefile,
8519          utils/Makefile, visitors/Makefile: change Makefile to relative path
8520  
8521 < 2004-09-28 21:55  tim
8521 > 2004-09-28 22:55  tim
8522  
8523          * src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c
8524          which cause headache in bulding libutils
8525  
8526 < 2004-09-28 18:24  tim
8526 > 2004-09-28 19:24  tim
8527  
8528          * src/applications/: BaseLattice.cpp, BaseLattice.hpp,
8529          Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h,
# Line 8373 | Line 8546
8546          change directory structure of application. Every executable file is
8547          replaced in seperate directory
8548  
8549 < 2004-09-28 17:15  gezelter
8549 > 2004-09-28 18:15  gezelter
8550  
8551          * lib/dummy: Keep that lib around, please.
8552  
8553 < 2004-09-28 17:14  gezelter
8553 > 2004-09-28 18:14  gezelter
8554  
8555          * Makefile, configure, ac-tools/configure.in, make/Make.conf.in:
8556          starting a configure version
8557  
8558 < 2004-09-28 16:08  tim
8558 > 2004-09-28 17:08  tim
8559  
8560          * src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90,
8561          UseTheForce/DarkSide/Makefile,
# Line 8391 | Line 8564
8564          brains/Makefile, brains/simulation_module.F90: move fortran files
8565          around to solve dependency problem
8566  
8567 < 2004-09-28 15:43  tim
8567 > 2004-09-28 16:43  tim
8568  
8569          * Makefile, src/UseTheForce/ForceFields.hpp,
8570          src/UseTheForce/Makefile, src/applications/BaseLattice.hpp,
# Line 8401 | Line 8574
8574          src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp,
8575          src/utils/Makefile: [no log message]
8576  
8577 < 2004-09-28 15:41  tim
8577 > 2004-09-28 16:41  tim
8578  
8579          * make/Makefile, scripts/sfmakedepend: fix fortran dependency
8580          problem
8581  
8582 < 2004-09-28 11:13  tim
8582 > 2004-09-28 12:13  tim
8583  
8584          * make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y,
8585          src/io/Makefile: add yacc and lex rules
8586  
8587 < 2004-09-27 15:24  tim
8587 > 2004-09-27 16:24  tim
8588  
8589          * make/Makefile: adding include path to F90Options
8590  
8591 < 2004-09-27 15:13  tim
8591 > 2004-09-27 16:13  tim
8592  
8593          * make/Makefile: change suffix from .cc to .cpp
8594  
8595 < 2004-09-24 11:27  tim
8595 > 2004-09-24 12:27  tim
8596  
8597          * src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp,
8598          UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp,
# Line 8486 | Line 8659
8659          visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp,
8660          visitors/ZconsVisitor.hpp: change the #include in source files
8661  
8662 < 2004-09-23 23:16  gezelter
8662 > 2004-09-24 00:16  gezelter
8663  
8664          * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
8665          src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,
# Line 8662 | Line 8835
8835          forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl,
8836          forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0
8837  
8838 < 2004-09-23 23:16  gezelter
8838 > 2004-09-24 00:16  gezelter
8839  
8840          * AUTHORS, ChangeLog, LICENSE, Makefile, README, configure,
8841          src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp,

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