1 |
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2004-07-23 15:31 tim |
1 |
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2004-10-20 17:54 tim |
2 |
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3 |
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* samples/lipid/5x5.bass: modify 5x5.bass |
3 |
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* ChangeLog, src/utils/PropertyMap.cpp, src/utils/PropertyMap.hpp, |
4 |
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test/utils/GenericDataTestCase.cpp, test/utils/Makefile, |
5 |
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test/utils/PropertyMapTestCase.cpp, |
6 |
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test/utils/PropertyMapTestCase.hpp, test/utils/UtilTest: |
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GenericData and PropertyMap pass unit test. |
8 |
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9 |
< |
2004-07-23 15:25 tim |
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> |
2004-10-20 16:52 gezelter |
10 |
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11 |
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* samples/water/tip3p_ice/: 200.in, tp3.bass: [no log message] |
11 |
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* src/UseTheForce/: DUFF.cpp, WATER.cpp, DarkSide/sticky.F90, |
12 |
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DarkSide/sticky_interface.h: fixed a fortran name problem |
13 |
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14 |
< |
2004-07-23 15:18 tim |
14 |
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2004-10-20 16:38 tim |
15 |
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16 |
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* samples/: water/ssde/ssde.bass, argon/500.bass, |
17 |
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argon/argonNVT.bass: [no log message] |
16 |
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* test/utils/: GenericData.hpp, GenericDataTestCase.cpp, |
17 |
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GenericDataTestCase.hpp, Makefile, PropertyMapTestCase.hpp, |
18 |
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UtilTest, UtilTest.cpp: adding generic data test case |
19 |
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20 |
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2004-07-23 15:12 tim |
20 |
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2004-10-20 16:16 chuckv |
21 |
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22 |
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* samples/water/: dimer/two.in, spce/spce.in, ssd/ssd.in, |
23 |
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ssde/ssde.in, tip3p_ice/tp3.in, tip4p/tp4.in: add init files |
22 |
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* configure, ac-tools/aclocal.m4, |
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src/UseTheForce/DarkSide/Makefile, |
24 |
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src/UseTheForce/DarkSide/mpiSimulation.F90, |
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src/UseTheForce/DarkSide/mpiSimulation_interface.h, |
26 |
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src/UseTheForce/DarkSide/simParallel.F90, |
27 |
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src/UseTheForce/DarkSide/simParallel_interface.h, |
28 |
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src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp: |
29 |
> |
Fortran/C++ interface de-obfuscation project appears to be |
30 |
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complete! Woo hoo! |
31 |
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32 |
< |
2004-07-23 15:10 tim |
32 |
> |
2004-10-20 15:47 chuckv |
33 |
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34 |
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* samples/minimizer/: ssdEM.in, tip4p_two.in: add init file |
34 |
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* src/UseTheForce/: fortranWrapDefines.hpp, fortranWrappers.cpp, |
35 |
> |
fortranWrappers.hpp: Fortran/C++ interface de-obfuscation project |
36 |
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continues |
37 |
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38 |
< |
2004-07-23 15:09 tim |
38 |
> |
2004-10-20 15:46 chuckv |
39 |
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40 |
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* samples/argon/: NVT.bass, argonNVT.bass, argonNVT.in: rename |
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NVT.bass to argonNVT.bass |
40 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
41 |
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UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
42 |
> |
UseTheForce/LJFF.cpp, UseTheForce/Makefile, UseTheForce/WATER.cpp, |
43 |
> |
UseTheForce/doForces_interface.h, |
44 |
> |
UseTheForce/notifyCutoffs_interface.h, UseTheForce/wrappers.F90, |
45 |
> |
UseTheForce/DarkSide/atype_interface.h, |
46 |
> |
UseTheForce/DarkSide/eam_interface.h, |
47 |
> |
UseTheForce/DarkSide/gb_interface.h, |
48 |
> |
UseTheForce/DarkSide/mpiSimulation_interface.h, |
49 |
> |
UseTheForce/DarkSide/shapes_interface.h, |
50 |
> |
UseTheForce/DarkSide/simulation_interface.h, |
51 |
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UseTheForce/DarkSide/sticky_interface.h, brains/ForceFields.cpp, |
52 |
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brains/SimInfo.cpp, brains/SimInfo.hpp: Fortran/C++ interface |
53 |
> |
de-obfuscation project (It is a very long story) |
54 |
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55 |
< |
2004-07-23 15:07 tim |
55 |
> |
2004-10-20 13:07 tim |
56 |
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57 |
< |
* samples/lipid/5x5.in: add 5x5.in |
57 |
> |
* ChangeLog, src/math/SquareMatrix.hpp, src/math/SquareMatrix3.hpp, |
58 |
> |
test/math/SquareMatrix3TestCase.cpp, |
59 |
> |
test/math/SquareMatrixTestCase.cpp, |
60 |
> |
test/math/SquareMatrixTestCase.hpp: Math library pass the unit test |
61 |
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62 |
< |
2004-07-23 15:06 tim |
62 |
> |
2004-10-20 00:52 tim |
63 |
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64 |
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* samples/alkane/: butane.in, init_butane.eor: add butane.in |
64 |
> |
* src/brains/: Snapshot.hpp, SnapshotManager.hpp: Snapshot and |
65 |
> |
SnapshotManager in design phase |
66 |
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67 |
< |
2004-07-23 14:57 gezelter |
67 |
> |
2004-10-19 23:54 gezelter |
68 |
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69 |
< |
* libBASS/Globals.cpp, samples/minimizer/ssdEM.bass, |
70 |
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samples/minimizer/tip4p_two.bass: changed minimizer keywords |
69 |
> |
* src/: brains/SimSetup.cpp, utils/StringUtils.cpp: namespace |
70 |
> |
problem prevented linking |
71 |
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72 |
< |
2004-07-23 14:34 gezelter |
72 |
> |
2004-10-19 23:54 gezelter |
73 |
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74 |
< |
* configure, ac-tools/configure.in: fixed typo |
74 |
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* src/UseTheForce/Shapes_FF.cpp: fixed include |
75 |
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76 |
< |
2004-07-23 14:32 gezelter |
76 |
> |
2004-10-19 23:26 gezelter |
77 |
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78 |
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* samples/minimizer/Makefile.in: fixed sample makefile |
78 |
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* src/utils/: Makefile, definitions.F90, definitions_module.F90, |
79 |
> |
oopseMPI.F90, oopseMPI_module.F90, status.F90, status_module.F90: |
80 |
> |
more fortran name mangling |
81 |
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82 |
< |
2004-07-23 14:31 gezelter |
82 |
> |
2004-10-19 23:23 gezelter |
83 |
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84 |
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* configure, ac-tools/configure.in, samples/minimizer/Makefile.in, |
52 |
< |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.bass, |
53 |
< |
samples/minimizer/tip4p_two.bass, samples/minimizer/water.mdl: |
54 |
< |
minimizer sample changes |
84 |
> |
* src/profiling/timing.F90: yet more fortran renaming |
85 |
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86 |
< |
2004-07-23 14:15 gezelter |
86 |
> |
2004-10-19 23:19 gezelter |
87 |
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|
88 |
< |
* configure, ac-tools/configure.in: removed beadLipid |
88 |
> |
* src/UseTheForce/: Makefile, doForces.F90, doForces_interface.h, |
89 |
> |
do_Forces.F90, do_Forces.h, notifyCutoffs.F90, |
90 |
> |
notifyCutoffs_interface.h, notifycutoffs_module_interface.h, |
91 |
> |
wrappers.F90: Fortran name cleanup continues |
92 |
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93 |
< |
2004-07-23 14:08 tim |
93 |
> |
2004-10-19 23:12 gezelter |
94 |
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|
95 |
< |
* samples/Makefile.in: remove beadLipid |
95 |
> |
* src/UseTheForce/DarkSide/: atype.F90, simulation.F90: fixing some |
96 |
> |
broken fortran stuff |
97 |
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|
98 |
< |
2004-07-23 14:03 chuckv |
98 |
> |
2004-10-19 23:02 gezelter |
99 |
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|
100 |
< |
* samples/metals/: Au_nanoparticle.eor, |
101 |
< |
Au_nanoparticle_coreshell_12-20.bass, |
102 |
< |
Au_nanoparticle_coreshell_12-20.in: Added core-shell nanoparticle |
103 |
< |
files. |
100 |
> |
* src/UseTheForce/DarkSide/: LJ.F90, Makefile, atype.F90, |
101 |
> |
atype_interface.h, atype_module.F90, atype_module_interface.h, |
102 |
> |
calc_LJ_FF.F90, calc_charge_charge.F90, calc_dipole_dipole.F90, |
103 |
> |
calc_eam.F90, calc_gb.F90, calc_reaction_field.F90, |
104 |
> |
calc_shapes.F90, calc_sticky_pair.F90, charge.F90, dipole.F90, |
105 |
> |
eam.F90, eam_interface.h, eam_module_inteface.h, gb.F90, |
106 |
> |
gb_interface.h, gb_module_interface.h, mpiSimulation.F90, |
107 |
> |
mpiSimulation_interface.h, mpiSimulation_module.F90, |
108 |
> |
mpisimulation_module_interface.h, reactionField.F90, shapes.F90, |
109 |
> |
shapes_interface.h, shapes_module.h, simulation.F90, |
110 |
> |
simulation_interface.h, simulation_module.F90, |
111 |
> |
simulation_module_interface.h, sticky.F90, sticky_interface.h, |
112 |
> |
sticky_pair_module_interface.h, switch_module.F90, switcheroo.F90: |
113 |
> |
name sanity on the fortran side |
114 |
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115 |
< |
2004-07-23 13:51 tim |
115 |
> |
2004-10-19 19:18 tim |
116 |
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|
117 |
< |
* samples/water/tip4p/TP4init.in: remove TP4init.in |
117 |
> |
* test/math/SquareMatrix3TestCase.hpp: [no log message] |
118 |
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119 |
< |
2004-07-23 13:50 tim |
119 |
> |
2004-10-19 18:01 tim |
120 |
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121 |
< |
* samples/water/tip4p/: Makefile.in, tp4.bass: change init file |
122 |
< |
name for tip4p and tip3p_ice |
121 |
> |
* src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
122 |
> |
src/math/SquareMatrix3.hpp, test/math/SquareMatrix3TestCase.cpp: |
123 |
> |
except diagonalize(), all of functions in math library pass the |
124 |
> |
test |
125 |
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126 |
< |
2004-07-23 13:48 tim |
126 |
> |
2004-10-19 17:43 chuckv |
127 |
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|
128 |
< |
* samples/water/ssde/: Makefile.in, SSDEinit.in: [no log message] |
128 |
> |
* src/UseTheForce/do_Forces.h: Added correct prototypes for |
129 |
> |
C-fortran interface functions. |
130 |
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131 |
< |
2004-07-23 13:48 tim |
131 |
> |
2004-10-19 17:37 chuckv |
132 |
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133 |
< |
* samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass: change |
134 |
< |
init file name for ssd |
133 |
> |
* src/UseTheForce/DarkSide/: atype_module_interface.h, |
134 |
> |
eam_module_inteface.h, gb_module_interface.h, |
135 |
> |
mpisimulation_module_interface.h, simulation_module_interface.h, |
136 |
> |
sticky_pair_module_interface.h: Added correct prototypes for |
137 |
> |
C-fortran interface functions. |
138 |
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|
139 |
< |
2004-07-23 13:46 tim |
139 |
> |
2004-10-19 16:28 tim |
140 |
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|
141 |
< |
* samples/water/spce/: Makefile.in, SPCEinit.in, spce.bass: remove |
142 |
< |
SPCEInit.in |
141 |
> |
* ChangeLog, src/math/Quaternion.hpp, src/math/RectMatrix.hpp, |
142 |
> |
src/math/SquareMatrix.hpp, src/math/Vector.hpp, |
143 |
> |
test/math/QuaternionTestCase.cpp, test/math/QuaternionTestCase.hpp, |
144 |
> |
test/math/RectMatrixTestCase.cpp, |
145 |
> |
test/math/SquareMatrix3TestCase.cpp, test/math/Vector3TestCase.cpp, |
146 |
> |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp: more |
147 |
> |
bugs get fixed at math library |
148 |
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149 |
< |
2004-07-23 13:45 tim |
149 |
> |
2004-10-19 15:43 chuckv |
150 |
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|
151 |
< |
* samples/water/dimer/: Makefile.in, two.bass, two.init: change |
152 |
< |
names for init file |
151 |
> |
* src/UseTheForce/: DarkSide/atype_module_interface.h, |
152 |
> |
DarkSide/eam_module_inteface.h, DarkSide/gb_module_interface.h, |
153 |
> |
DarkSide/mpisimulation_module_interface.h, |
154 |
> |
DarkSide/simulation_module_interface.h, |
155 |
> |
DarkSide/sticky_pair_module_interface.h, DarkSide/calc_eam.F90, |
156 |
> |
DarkSide/atype_module.F90, DarkSide/calc_gb.F90, |
157 |
> |
DarkSide/calc_sticky_pair.F90, DarkSide/mpiSimulation_module.F90, |
158 |
> |
DarkSide/simulation_module.F90, do_Forces.F90, |
159 |
> |
fortranWrapDefines.hpp, mpiComponentPlan.h, notifyCutoffs.F90, |
160 |
> |
notifycutoffs_module_interface.h: Added new files for fortran |
161 |
> |
interface. |
162 |
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163 |
< |
2004-07-23 13:40 tim |
163 |
> |
2004-10-19 15:43 gezelter |
164 |
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|
165 |
< |
* samples/lipid/: 5x5.bass, 5x5.eor, Makefile.in, init_5x5.eor: |
102 |
< |
change init file name in lipid directory |
165 |
> |
* src/UseTheForce/Makefile: regressing |
166 |
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|
167 |
< |
2004-07-23 13:36 tim |
167 |
> |
2004-10-19 15:40 gezelter |
168 |
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|
169 |
< |
* samples/argon/init_argon.eor: remove init_argon.eor |
169 |
> |
* src/: UseTheForce/DarkSide/calc_shapes.F90, |
170 |
> |
UseTheForce/DarkSide/shapes_module.h, utils/StringUtils.cpp: |
171 |
> |
working on shapes for portability |
172 |
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173 |
< |
2004-07-23 13:34 tim |
173 |
> |
2004-10-19 15:40 gezelter |
174 |
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|
175 |
< |
* samples/: alkane/Makefile.in, alkane/butane.bass, |
111 |
< |
alkane/butane.eor, argon/500.eor, argon/ar864.eor: [no log message] |
175 |
> |
* src/UseTheForce/: Makefile, Shapes_FF.cpp: working on shapes |
176 |
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177 |
< |
2004-07-23 13:33 tim |
177 |
> |
2004-10-19 13:21 chrisfen |
178 |
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179 |
< |
* samples/argon/Makefile.in: remove eor file |
179 |
> |
* src/utils/: StringUtils.cpp, StringUtils.hpp: changed around |
180 |
> |
findBegin |
181 |
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182 |
< |
2004-07-23 13:31 tim |
182 |
> |
2004-10-18 23:34 tim |
183 |
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184 |
< |
* samples/argon/: Makefile.in, argon.bass, argon.eor, argonEM.bass: |
185 |
< |
change names for argon |
184 |
> |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp: more bugs |
185 |
> |
are fixed in Vector class |
186 |
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187 |
< |
2004-07-23 11:47 tim |
187 |
> |
2004-10-18 23:28 tim |
188 |
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|
189 |
< |
* samples/water/ssde/SSDEinit.in: [no log message] |
189 |
> |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp: fix |
190 |
> |
some bugs in RectMatrixTestCase |
191 |
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192 |
< |
2004-07-23 11:45 tim |
192 |
> |
2004-10-18 23:21 tim |
193 |
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|
194 |
< |
* samples/water/ssde/SSDEinit.in: add init file for ssde |
194 |
> |
* src/math/Vector.hpp, test/math/RectMatrixTestCase.cpp, |
195 |
> |
test/math/RectMatrixTestCase.hpp, test/math/Vector3TestCase.cpp, |
196 |
> |
test/math/Vector3TestCase.hpp, test/math/VectorTestCase.cpp, |
197 |
> |
test/math/VectorTestCase.hpp: implement more test cases |
198 |
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|
199 |
< |
2004-07-23 11:43 chuckv |
199 |
> |
2004-10-18 18:13 tim |
200 |
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|
201 |
< |
* libmdtools/calc_eam.F90: Fixed bug in calc_eam with mixtures and |
202 |
< |
cutoffs associated with mixture. |
201 |
> |
* ChangeLog, make/Doxyfile, src/math/Matrix3x3d.hpp, |
202 |
> |
src/math/RectMatrix.hpp, src/math/SquareMatrix.hpp, |
203 |
> |
src/math/SquareMatrix3.hpp, src/math/Vector.hpp, |
204 |
> |
src/utils/StringTokenizer.hpp, test/math/Makefile, |
205 |
> |
test/math/VectorTestCase.cpp, test/math/VectorTestCase.hpp: more |
206 |
> |
tests on math library |
207 |
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208 |
< |
2004-07-23 10:35 tim |
208 |
> |
2004-10-18 16:03 tim |
209 |
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|
210 |
< |
* libmdtools/: AtomVisitor.cpp, AtomVisitor.hpp: support SSD_E |
211 |
< |
SSD_RF SSD1 |
210 |
> |
* test/math/: Makefile, QuaternionTestCase.cpp, |
211 |
> |
QuaternionTestCase.hpp, RectMatrixTestCase.cpp, |
212 |
> |
SquareMatrix3TestCase.cpp, Vector3TestCase.cpp, |
213 |
> |
Vector3TestCase.hpp, VectorTestCase.cpp, VectorTestCase.hpp: adding |
214 |
> |
more testing units |
215 |
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|
216 |
< |
2004-07-23 09:53 tim |
216 |
> |
2004-10-18 12:07 tim |
217 |
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|
218 |
< |
* libmdtools/AtomVisitor.cpp: SSDVisitor support SSD_RF, SSD_E, |
219 |
< |
SSD1 now |
218 |
> |
* src/: brains/SimSetup.hpp, io/FileReader.hpp, math/Euler3.cpp, |
219 |
> |
math/Euler3.hpp, math/Quaternion.hpp, math/SquareMatrix3.hpp, |
220 |
> |
math/Vector3.hpp, types/ShapeType.cpp, types/ShapeType.hpp, |
221 |
> |
utils/GenericFactory.hpp: fix some bugs in Quaternion class |
222 |
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|
223 |
< |
2004-07-23 09:19 tim |
146 |
< |
|
147 |
< |
* libmdtools/ZConsReader.cpp: remove ^M from ZConsReader.cpp |
223 |
> |
2004-10-18 11:30 gezelter |
224 |
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|
225 |
< |
2004-07-23 09:18 tim |
225 |
> |
* src/math/: RealSphericalHarmonic.cpp, RealSphericalHarmonic.hpp: |
226 |
> |
Your basic run of the mill real-valued versions of Y_l^m(\theta, |
227 |
> |
\phi) |
228 |
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|
229 |
< |
* samples/lipid/5x5.bass: remove unsupport keyword |
229 |
> |
2004-10-18 11:29 gezelter |
230 |
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|
231 |
< |
2004-07-22 16:01 chuckv |
231 |
> |
* src/: math/Makefile, math/Matrix3x3d.hpp, math/Vector3.hpp, |
232 |
> |
types/Makefile, types/ShapeType.cpp, types/ShapeType.hpp, |
233 |
> |
utils/StringUtils.cpp, utils/StringUtils.hpp: Working on getting |
234 |
> |
Shapes into OOPSE |
235 |
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|
236 |
< |
* samples/metals/: init_Au_bulk.in, init_Au_nanoparticle.in: |
156 |
< |
Changed init files to be more OOPSE like... |
236 |
> |
2004-10-18 10:21 gezelter |
237 |
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|
238 |
< |
2004-07-22 10:11 gezelter |
238 |
> |
* src/types/: ShapeType.cpp, ShapeType.hpp: Added ShapeType |
239 |
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|
240 |
< |
* configure, ac-tools/configure.in: added sample directory |
240 |
> |
2004-10-18 00:23 tim |
241 |
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242 |
< |
2004-07-22 10:06 chrisfen |
242 |
> |
* test/math/VectorTestCase.hpp: adding vector test case |
243 |
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|
244 |
< |
* src/Makefile.in: fixed icc7 incompatibility in linking |
244 |
> |
2004-10-18 00:23 tim |
245 |
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|
246 |
< |
2004-07-21 17:03 chrisfen |
246 |
> |
* src/utils/GenericFactory.hpp: adding generic factory and vector |
247 |
> |
test case |
248 |
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|
249 |
< |
* samples/water/: Makefile.in, tip3p_ice/200.in, |
169 |
< |
tip3p_ice/Makefile.in, tip3p_ice/tp3.bass, tip3p_ice/water.mdl: |
170 |
< |
Added tip3p_ice to Makefile |
249 |
> |
2004-10-16 20:19 tim |
250 |
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|
251 |
< |
2004-07-21 16:46 chuckv |
251 |
> |
* src/math/: Quaternion.hpp, RectMatrix.hpp, SquareMatrix.hpp, |
252 |
> |
SquareMatrix3.hpp, Vector.hpp, Vector3.hpp: math library in |
253 |
> |
progress |
254 |
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|
255 |
< |
* samples/metals/: Au.bass, Au.eor, Au_bulk_FBD.bass, |
175 |
< |
Au_bulk_voter.bass, Au_nanoparticle.bass, Au_nanoparticle.eor, |
176 |
< |
init_Au_bulk.in, init_Au_nanoparticle.in, init_au.in: Added sample |
177 |
< |
files for bulk metals and a bass file for both voter and FBD |
178 |
< |
formulations of EAM. |
255 |
> |
2004-10-15 20:31 tim |
256 |
|
|
257 |
< |
2004-07-21 14:53 gezelter |
257 |
> |
* src/math/Quaternion.hpp: add quaternion class |
258 |
|
|
259 |
< |
* samples/water/dimer/two.bass: Checked a bug where eor file wasn't |
183 |
< |
being written at the end of the run |
259 |
> |
2004-10-15 16:11 tim |
260 |
|
|
261 |
< |
2004-07-21 14:53 gezelter |
261 |
> |
* test/io/: DUFF.frc, IfstrstreamTestCase.cpp, |
262 |
> |
IfstrstreamTestCase.hpp: adding test file |
263 |
|
|
264 |
< |
* libmdtools/Integrator.cpp: Fixed a bug where eor file wasn't |
188 |
< |
being written at the end of the run |
264 |
> |
2004-10-15 16:10 tim |
265 |
|
|
266 |
< |
2004-07-21 09:11 gezelter |
266 |
> |
* src/io/basic_ifstrstream.hpp: fix a bunch of bugs |
267 |
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|
268 |
< |
* README: [no log message] |
268 |
> |
2004-10-15 15:42 tim |
269 |
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|
270 |
< |
2004-07-21 09:08 gezelter |
270 |
> |
* src/io/basic_ifstrstream.hpp: change const_cast to statc_const |
271 |
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|
272 |
< |
* samples/argon/machines: cleaning up for export |
272 |
> |
2004-10-15 15:35 tim |
273 |
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|
274 |
< |
2004-07-21 09:04 gezelter |
274 |
> |
* src/io/basic_ifstrstream.hpp: fix a bug in basic_ifstrstream.hpp |
275 |
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|
276 |
< |
* NEWS, README: cleaning up for export |
276 |
> |
2004-10-15 15:34 tim |
277 |
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|
278 |
< |
2004-07-21 08:45 gezelter |
278 |
> |
* test/io/: IfstrstreamTestCase.cpp, Makefile: forget to use |
279 |
> |
namespace oopse |
280 |
|
|
281 |
< |
* configure, ac-tools/configure.in: removing staticProps from cvs |
205 |
< |
tree |
281 |
> |
2004-10-15 14:38 chuckv |
282 |
|
|
283 |
< |
2004-07-20 12:07 gezelter |
283 |
> |
* configure, ac-tools/aclocal.m4: Changed optimization flags for |
284 |
> |
XLF and XLC. |
285 |
|
|
286 |
< |
* configure, ac-tools/aclocal.m4, utils/Makefile.in, |
210 |
< |
utils/quickLate.c, utils/sysbuilder/Makefile.in: [no log message] |
286 |
> |
2004-10-15 13:28 tim |
287 |
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|
288 |
< |
2004-07-20 10:17 gezelter |
288 |
> |
* test/io/: IfstrstreamTestCase.cpp, IfstrstreamTestCase.hpp: |
289 |
> |
adding ifstrstream test case |
290 |
|
|
291 |
< |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
215 |
< |
third-party/gnugetopt.h, utils/getopt.c, utils/getopt1.c, |
216 |
< |
utils/gnugetopt.h: fixing getopt_long |
291 |
> |
2004-10-15 13:20 tim |
292 |
|
|
293 |
< |
2004-07-19 16:58 gezelter |
293 |
> |
* src/io/basic_ifstrstream.hpp: fix include |
294 |
|
|
295 |
< |
* configure, ac-tools/configure.in, libmdtools/ReadWrite.hpp, |
221 |
< |
libmdtools/ZConsWriter.hpp, src/Makefile.in, |
222 |
< |
third-party/gnugetopt.h, utils/Dump2XYZCmd.c, utils/Make.dep, |
223 |
< |
utils/Makefile.in, utils/sysbuilder/Makefile.in, |
224 |
< |
utils/sysbuilder/latticeBuilder.cpp: [no log message] |
295 |
> |
2004-10-15 13:18 tim |
296 |
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|
297 |
< |
2004-07-19 16:52 tim |
297 |
> |
* src/math/SquareMatrix.hpp: fix incompatible declaration in jacobi |
298 |
|
|
299 |
< |
* utils/quickLate.c: minor fix of format string in quicklate.c |
299 |
> |
2004-10-15 13:17 tim |
300 |
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|
301 |
< |
2004-07-19 16:30 tim |
301 |
> |
* test/math/: Makefile, RectMatrixTestCase.cpp: adding Makefile |
302 |
|
|
303 |
< |
* utils/zsub: remove zsub from cvs tree |
303 |
> |
2004-10-15 13:16 tim |
304 |
|
|
305 |
< |
2004-07-19 16:25 tim |
305 |
> |
* test/io/: Makefile, ifstrstreamTestCase.cpp, |
306 |
> |
ifstrstreamTestCase.hpp: adding test case for ifstrstream |
307 |
|
|
308 |
< |
* libmdtools/ZConstraint.cpp, utils/Dump2XYZ.cpp: remove some |
237 |
< |
comment lines |
308 |
> |
2004-10-15 10:37 tim |
309 |
|
|
310 |
< |
2004-07-19 16:00 tim |
310 |
> |
* test/io/: IOTest.cpp, ifstrstreamTestCase.cpp, |
311 |
> |
ifstrstreamTestCase.hpp: add ifstrstreamTestCase |
312 |
|
|
313 |
< |
* libmdtools/OOPSEMinimizer.hpp: remove an extra semicolon from |
242 |
< |
OOPSEMinimizer.hpp |
313 |
> |
2004-10-15 10:20 tim |
314 |
|
|
315 |
< |
2004-07-19 13:55 gezelter |
315 |
> |
* src/io/basic_ifstrstream.hpp: add checkFilename Option |
316 |
|
|
317 |
< |
* libBASS/y.tab.h: Shouldn't have been in CVS |
317 |
> |
2004-10-15 10:19 tim |
318 |
|
|
319 |
< |
2004-07-19 13:54 gezelter |
319 |
> |
* test/math/: RectMatrixTestCase.cpp, RectMatrixTestCase.hpp, |
320 |
> |
SquareMatrixTestCase.cpp, SquareMatrixTestCase.hpp: add |
321 |
> |
SquareMatrixTestCase class |
322 |
|
|
323 |
< |
* libBASS/y.tab.h, libmdtools/ForceFields.cpp: Fix for |
251 |
< |
thermodynamic integration of rigid bodies |
323 |
> |
2004-10-15 02:52 tim |
324 |
|
|
325 |
< |
2004-07-19 12:00 gezelter |
325 |
> |
* src/io/basic_ifstrstream.hpp: adding basic_ifstrstream |
326 |
|
|
327 |
< |
* libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: These can be |
256 |
< |
generated via lex and yacc at compile time |
327 |
> |
2004-10-14 18:28 tim |
328 |
|
|
329 |
< |
2004-07-19 11:47 gezelter |
329 |
> |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp, SquareMatrix3.hpp, |
330 |
> |
Vector.hpp: math library in progress |
331 |
|
|
332 |
< |
* libBASS/BASSlex.c, libBASS/BASSyacc.c, libBASS/BASSyacc.h, |
261 |
< |
libBASS/make_nodes.c, libBASS/y.tab.h, libmdtools/Makefile.in, |
262 |
< |
libmdtools/MatVec3.c, src/Makefile.in: [no log message] |
332 |
> |
2004-10-14 18:27 tim |
333 |
|
|
334 |
< |
2004-07-19 11:32 gezelter |
334 |
> |
* src/io/FileReader.hpp: FileReader in progress |
335 |
|
|
336 |
< |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
267 |
< |
third-party/gnugetopt.h, utils/Makefile.in, |
268 |
< |
utils/sysbuilder/Makefile.in: changes for gnu getopt and fixed |
269 |
< |
SPRNG configure script |
336 |
> |
2004-10-13 18:53 tim |
337 |
|
|
338 |
< |
2004-07-16 16:49 gezelter |
338 |
> |
* src/math/: RectMatrix.hpp, SquareMatrix.hpp: Matrix in progress, |
339 |
> |
test in isOrthogonal of SquareMatrix is failed by some reasons |
340 |
|
|
341 |
< |
* libBASS/: BASSlex.c, BASSyacc.c, BASSyacc.h: fixing for machines |
274 |
< |
that don't have lex and yacc |
341 |
> |
2004-10-13 17:28 tim |
342 |
|
|
343 |
< |
2004-07-16 15:55 gezelter |
343 |
> |
* src/utils/: PropertyMap.cpp, PropertyMap.hpp: adding PropertyMap |
344 |
> |
class |
345 |
|
|
346 |
< |
* Makefile: Makefiles don't belong in cvs repository |
346 |
> |
2004-10-13 17:27 tim |
347 |
|
|
348 |
< |
2004-07-16 15:54 gezelter |
348 |
> |
* test/math/: MainTest.cpp, RectMatrixTestCase.cpp, |
349 |
> |
RectMatrixTestCase.hpp: adding testing unit |
350 |
|
|
351 |
< |
* Makefile, forceFields/Makefile, libBASS/Makefile, |
283 |
< |
libmdtools/Makefile, samples/Makefile, src/Makefile, |
284 |
< |
third-party/Makefile, utils/Makefile, utils/sysbuilder/Makefile: |
285 |
< |
Makefiles don't belong in repository |
351 |
> |
2004-10-13 17:24 tim |
352 |
|
|
353 |
< |
2004-07-16 15:49 gezelter |
353 |
> |
* src/math/: RectMatrix.hpp, Vector.hpp: adding RectMatrix |
354 |
|
|
355 |
+ |
2004-10-13 01:51 tim |
356 |
+ |
|
357 |
+ |
* src/math/: SquareMatrix.hpp, SquareMatrix3.hpp, Vector.hpp, |
358 |
+ |
Vector3.hpp: refactory vector and matrix classes |
359 |
+ |
|
360 |
+ |
2004-10-13 01:50 tim |
361 |
+ |
|
362 |
+ |
* src/math/Vector3d.hpp: Remove some Makefile.in |
363 |
+ |
|
364 |
+ |
2004-10-12 18:57 tim |
365 |
+ |
|
366 |
+ |
* src/math/: Matrix3x3d.hpp, Vector3d.hpp: add Vector3d.hpp and |
367 |
+ |
Matrix3x3d.hpp |
368 |
+ |
|
369 |
+ |
2004-10-12 14:08 tim |
370 |
+ |
|
371 |
+ |
* doc/: cppstyle.html, style.css: adding c++ coding style |
372 |
+ |
|
373 |
+ |
2004-10-11 17:15 tim |
374 |
+ |
|
375 |
+ |
* src/: constraints/AbstractClasses.hpp, |
376 |
+ |
integrators/AbstractClasses.hpp, primitives/AbstractClasses.hpp: |
377 |
+ |
change #include "mpi.h" to #include <mpi.h> in AbstractClasses.hpp |
378 |
+ |
|
379 |
+ |
2004-10-11 16:54 tim |
380 |
+ |
|
381 |
+ |
* scripts/filepp: fix a bug in filepp |
382 |
+ |
|
383 |
+ |
2004-10-11 16:13 tim |
384 |
+ |
|
385 |
+ |
* make/Makefile.in: using filepp to generate dependencies instead |
386 |
+ |
of compilers |
387 |
+ |
|
388 |
+ |
2004-10-11 16:10 tim |
389 |
+ |
|
390 |
+ |
* scripts/filepp: filepp can be used to generate dependencies for |
391 |
+ |
c/c++ now |
392 |
+ |
|
393 |
+ |
2004-10-11 13:40 tim |
394 |
+ |
|
395 |
+ |
* make/Makefile.in: remove -module from F90Options |
396 |
+ |
|
397 |
+ |
2004-10-11 13:01 tim |
398 |
+ |
|
399 |
+ |
* make/Makefile.in: adding rules to move fortran 90 module to |
400 |
+ |
target directory |
401 |
+ |
|
402 |
+ |
2004-10-11 10:43 gezelter |
403 |
+ |
|
404 |
+ |
* make/Makefile.in: fixed makefile.in |
405 |
+ |
|
406 |
+ |
2004-10-11 09:51 tim |
407 |
+ |
|
408 |
+ |
* scripts/filepp: remove "use bytes" which causes problem in sgi |
409 |
+ |
machine |
410 |
+ |
|
411 |
+ |
2004-10-11 09:26 tim |
412 |
+ |
|
413 |
+ |
* forceFields/Makefile: add Makefile |
414 |
+ |
|
415 |
+ |
2004-10-11 09:23 tim |
416 |
+ |
|
417 |
+ |
* samples/: water/dimer/Makefile, water/spce/Makefile, |
418 |
+ |
water/ssd/Makefile, water/ssde/Makefile, water/tip3p_ice/Makefile, |
419 |
+ |
water/tip4p/Makefile, zcons/Makefile: fix Makefile under water |
420 |
+ |
directory |
421 |
+ |
|
422 |
+ |
2004-10-11 09:23 tim |
423 |
+ |
|
424 |
+ |
* samples/argon/Makefile: remove argon.dump and argon.eor from |
425 |
+ |
Makefile |
426 |
+ |
|
427 |
+ |
2004-10-09 01:01 tim |
428 |
+ |
|
429 |
+ |
* samples/: alkane/Makefile.in, argon/Makefile.in, |
430 |
+ |
lipid/Makefile.in, metals/Makefile.in, minimizer/Makefile.in: |
431 |
+ |
Remove some Makefile.in |
432 |
+ |
|
433 |
+ |
2004-10-08 18:15 tim |
434 |
+ |
|
435 |
+ |
* make/Makefile.in: [no log message] |
436 |
+ |
|
437 |
+ |
2004-10-08 17:51 tim |
438 |
+ |
|
439 |
+ |
* make/Makefile.in: fix make install |
440 |
+ |
|
441 |
+ |
2004-10-08 17:10 tim |
442 |
+ |
|
443 |
+ |
* make/Makefile.in: adding make install |
444 |
+ |
|
445 |
+ |
2004-10-08 17:04 tim |
446 |
+ |
|
447 |
|
* samples/: alkane/Makefile, argon/Makefile, lipid/Makefile, |
448 |
< |
metals/Makefile: Makefiles don't belong in repository |
448 |
> |
metals/Makefile, minimizer/Makefile, water/Makefile.in, |
449 |
> |
water/dimer/Makefile, water/dimer/Makefile.in, water/spce/Makefile, |
450 |
> |
water/spce/Makefile.in, water/ssd/Makefile, water/ssd/Makefile.in, |
451 |
> |
water/ssde/Makefile, water/ssde/Makefile.in, |
452 |
> |
water/tip3p_ice/Makefile, water/tip3p_ice/Makefile.in, |
453 |
> |
water/tip4p/Makefile, water/tip4p/Makefile.in, zcons/Makefile, |
454 |
> |
zcons/Makefile.in: add Makefile to sample directory |
455 |
|
|
456 |
< |
2004-07-16 15:20 chrisfen |
456 |
> |
2004-10-06 18:03 gezelter |
457 |
|
|
458 |
< |
* Makefile, configure, ac-tools/configure.in, forceFields/Makefile, |
459 |
< |
libBASS/Makefile, libmdtools/Makefile, samples/alkane/Makefile, |
296 |
< |
samples/argon/Makefile, samples/lipid/Makefile, |
297 |
< |
samples/metals/Makefile, src/Makefile, utils/Makefile, |
298 |
< |
utils/sysbuilder/Makefile: Updated configure for new samples |
458 |
> |
* src/utils/: getopt.c, getopt1.c, gnugetopt.h: moved the getopt |
459 |
> |
stuff |
460 |
|
|
461 |
< |
2004-07-16 14:57 chrisfen |
461 |
> |
2004-10-06 18:03 gezelter |
462 |
|
|
463 |
< |
* samples/water/tip4p/Makefile.in: tip4p makefile.in added |
463 |
> |
* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
464 |
> |
make/Doxyfile, src/applications/getopt.c, |
465 |
> |
src/applications/getopt1.c, src/applications/gnugetopt.h: more |
466 |
> |
build fixes |
467 |
|
|
468 |
< |
2004-07-16 14:57 chrisfen |
468 |
> |
2004-10-06 17:20 tim |
469 |
|
|
470 |
< |
* samples/water/ssde/: 256init.in, Makefile.in, ssde.bass: ssde |
307 |
< |
makefile.in added |
470 |
> |
* make/: Doxyfile, Makefile.in: adding doxygen configuration file |
471 |
|
|
472 |
< |
2004-07-16 14:57 chrisfen |
472 |
> |
2004-10-06 17:19 tim |
473 |
|
|
474 |
< |
* samples/water/ssd/: Makefile.in, init_ssd.eor, ssd.bass, |
475 |
< |
water.mdl: ssd files sorted added |
474 |
> |
* scripts/filepp: filepp can handle different fortran module case |
475 |
> |
and suffix |
476 |
|
|
477 |
< |
2004-07-16 14:57 chrisfen |
477 |
> |
2004-10-06 16:27 gezelter |
478 |
|
|
479 |
< |
* samples/water/spce/Makefile.in: spce makefile.in added |
479 |
> |
* src/restraints/Restraints.cpp: Chris doesn't know about the |
480 |
> |
OOPSE-2.0 directory structure yet |
481 |
|
|
482 |
< |
2004-07-16 14:56 chrisfen |
482 |
> |
2004-10-06 16:27 gezelter |
483 |
|
|
484 |
< |
* samples/water/dimer/: Makefile.in, two.bass, two.init, water.mdl: |
321 |
< |
dimer files added |
484 |
> |
* ChangeLog: Yeah yeah, we'lll get around to it later |
485 |
|
|
486 |
< |
2004-07-16 14:56 chrisfen |
486 |
> |
2004-10-06 16:22 gezelter |
487 |
|
|
488 |
< |
* samples/water/: 200.in, Makefile, Makefile.in, init_ssd.eor, |
489 |
< |
spce.bass, spce.eor, ssd.bass, ssd.eor, tim.bass, tim.eor, |
327 |
< |
tim.init, tim.xyz, tip3p.bass, tip3p.eor, tip3p.init, two.bass, |
328 |
< |
two.eor, two.init, two.xyz, water.mdl: Cleaned up this file |
329 |
< |
considerably |
488 |
> |
* configure, ac-tools/configure.in, ac-tools/fortran90.m4, |
489 |
> |
make/Makefile.in: cleaning up build process |
490 |
|
|
491 |
< |
2004-07-16 13:57 gezelter |
491 |
> |
2004-10-06 15:01 chrisfen |
492 |
|
|
493 |
< |
* AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README, |
494 |
< |
configure, ac-tools/Make.conf.in, ac-tools/aclocal.m4, |
495 |
< |
ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in, |
496 |
< |
ac-tools/fortran90.m4, ac-tools/install-sh, ac-tools/shtool, |
497 |
< |
forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl, |
498 |
< |
forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl, |
499 |
< |
forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl, |
493 |
> |
* src/restraints/Restraints.cpp: made the file reading in |
494 |
> |
restraints more intelligent - no longer gives uninformative seg |
495 |
> |
faults |
496 |
> |
|
497 |
> |
2004-10-06 14:55 gezelter |
498 |
> |
|
499 |
> |
* src/applications/simpleBuilder/Make.ftemp.old: cleaning up |
500 |
> |
|
501 |
> |
2004-10-06 14:51 gezelter |
502 |
> |
|
503 |
> |
* LICENSE, MPIobj/dummy, make/Makefile, obj/dummy, |
504 |
> |
scripts/cleanSrc, src/brains/Makedepend: Cleaning up a bit |
505 |
> |
|
506 |
> |
2004-10-06 13:53 tim |
507 |
> |
|
508 |
> |
* make/: Makefile, Makefile.in: fix make statistics |
509 |
> |
|
510 |
> |
2004-10-06 13:18 tim |
511 |
> |
|
512 |
> |
* make/: Makefile, Makefile.in: adding GNU make functions to |
513 |
> |
combine all of the static libraries to a big library |
514 |
> |
|
515 |
> |
2004-10-05 17:57 tim |
516 |
> |
|
517 |
> |
* make/: Makefile, Makefile.in: adding shared library flag |
518 |
> |
|
519 |
> |
2004-10-05 14:37 tim |
520 |
> |
|
521 |
> |
* src/: Makefile, UseTheForce/Makefile, |
522 |
> |
UseTheForce/mpiSimulation_module.F90, |
523 |
> |
UseTheForce/DarkSide/Makefile, |
524 |
> |
UseTheForce/DarkSide/mpiSimulation_module.F90, math/Makefile: move |
525 |
> |
mpiSimulation_module to DarkSide |
526 |
> |
|
527 |
> |
2004-10-05 14:35 tim |
528 |
> |
|
529 |
> |
* make/: Makefile, Makefile.in: building MPI version;using static |
530 |
> |
library instead of shared library |
531 |
> |
|
532 |
> |
2004-10-05 09:14 tim |
533 |
> |
|
534 |
> |
* make/: Makefile, Makefile.in: pass __FORTRAN90 instead of __F90 |
535 |
> |
to filepp |
536 |
> |
|
537 |
> |
2004-10-04 15:56 tim |
538 |
> |
|
539 |
> |
* make/: Makefile, Makefile.in: add make cvslog |
540 |
> |
|
541 |
> |
2004-10-04 11:24 gezelter |
542 |
> |
|
543 |
> |
* make/: Makefile, Makefile.in: more work on the parallel build |
544 |
> |
|
545 |
> |
2004-10-04 11:06 gezelter |
546 |
> |
|
547 |
> |
* make/: Makefile, Makefile.in: changes to backport declare flags |
548 |
> |
|
549 |
> |
2004-10-04 10:27 gezelter |
550 |
> |
|
551 |
> |
* src/UseTheForce/: ForceFields.hpp, Shapes_FF.cpp, |
552 |
> |
DarkSide/Makefile, DarkSide/calc_shapes.F90: Started work merging |
553 |
> |
shapes |
554 |
> |
|
555 |
> |
2004-10-01 23:40 tim |
556 |
> |
|
557 |
> |
* scripts/: filepp, sfmakedepend: remove sfmakedepend from cvs tree |
558 |
> |
|
559 |
> |
2004-10-01 23:22 tim |
560 |
> |
|
561 |
> |
* make/: Makefile, Makefile.in: add oopse_ as library prefix |
562 |
> |
|
563 |
> |
2004-10-01 16:59 tim |
564 |
> |
|
565 |
> |
* make/: Makefile, Makefile.in: fix a space trimming bug in filepp |
566 |
> |
|
567 |
> |
2004-10-01 16:22 gezelter |
568 |
> |
|
569 |
> |
* Makefile, ac-tools/aclocal.m4, make/Makefile, make/Makefile.in: A |
570 |
> |
few minor build changes |
571 |
> |
|
572 |
> |
2004-10-01 16:11 tim |
573 |
> |
|
574 |
> |
* scripts/filepp: adding fortran90 make dependency tool |
575 |
> |
|
576 |
> |
2004-09-30 10:41 tim |
577 |
> |
|
578 |
> |
* make/: Makefile, Makefile.in: make clean is smart enough to only |
579 |
> |
remove object files belong to current package. turn off silent |
580 |
> |
mode |
581 |
> |
|
582 |
> |
2004-09-29 16:55 tim |
583 |
> |
|
584 |
> |
* src/: Makefile, UseTheForce/Makefile, |
585 |
> |
UseTheForce/DarkSide/Makefile, applications/dump2Xyz/Makefile, |
586 |
> |
applications/oopse/Makefile, applications/simpleBuilder/Makefile, |
587 |
> |
brains/Makedepend, brains/Makefile, constraints/Makefile, |
588 |
> |
integrators/Makefile, io/Makefile, math/Makefile, |
589 |
> |
minimizers/Makefile, primitives/Makefile, profiling/Makefile, |
590 |
> |
restraints/Makefile, types/Makefile, utils/Makefile, |
591 |
> |
visitors/Makefile: define DEV_ROOT as relative path |
592 |
> |
|
593 |
> |
2004-09-29 16:54 tim |
594 |
> |
|
595 |
> |
* make/: Makefile, Makefile.in: get the relative path by shell |
596 |
> |
script |
597 |
> |
|
598 |
> |
2004-09-29 16:32 tim |
599 |
> |
|
600 |
> |
* make/Makefile: eliminate DEV_ROOT by relative path |
601 |
> |
|
602 |
> |
2004-09-29 13:37 tim |
603 |
> |
|
604 |
> |
* make/Makefile.in: add PackageLibs; fix dependency rule |
605 |
> |
|
606 |
> |
2004-09-29 12:57 gezelter |
607 |
> |
|
608 |
> |
* configure, ac-tools/configure.in: updates |
609 |
> |
|
610 |
> |
2004-09-29 12:56 gezelter |
611 |
> |
|
612 |
> |
* make/: Make.conf.in, Makefile.in: Working on make stuff |
613 |
> |
|
614 |
> |
2004-09-29 12:46 tim |
615 |
> |
|
616 |
> |
* Makefile: If makefile does not exist, print error message |
617 |
> |
|
618 |
> |
2004-09-29 12:12 tim |
619 |
> |
|
620 |
> |
* make/: Make.conf.in, Makefile: fix dependencies rule |
621 |
> |
|
622 |
> |
2004-09-29 10:58 gezelter |
623 |
> |
|
624 |
> |
* Makefile, make/Makefile: still working on build process |
625 |
> |
|
626 |
> |
2004-09-29 10:00 tim |
627 |
> |
|
628 |
> |
* make/Makefile: add print statment to rules |
629 |
> |
|
630 |
> |
2004-09-29 09:59 tim |
631 |
> |
|
632 |
> |
* src/: UseTheForce/Makefile, UseTheForce/DarkSide/Makefile, |
633 |
> |
applications/dump2Xyz/Makefile, applications/oopse/Makefile, |
634 |
> |
applications/simpleBuilder/Makefile, brains/Makefile, |
635 |
> |
constraints/Makefile, integrators/Makefile, io/Makefile, |
636 |
> |
math/Makefile, minimizers/Makefile, primitives/Makefile, |
637 |
> |
profiling/Makefile, restraints/Makefile, types/Makefile, |
638 |
> |
utils/Makefile, visitors/Makefile: change Makefile to relative path |
639 |
> |
|
640 |
> |
2004-09-28 21:55 tim |
641 |
> |
|
642 |
> |
* src/utils/: StringUtils.c, StringUtils.h: remove StringUtils.c |
643 |
> |
which cause headache in bulding libutils |
644 |
> |
|
645 |
> |
2004-09-28 18:24 tim |
646 |
> |
|
647 |
> |
* src/applications/: BaseLattice.cpp, BaseLattice.hpp, |
648 |
> |
Dump2XYZ.cpp, Dump2XYZ.ggo, Dump2XYZCmd.c, Dump2XYZCmd.h, |
649 |
> |
Lattice.cpp, Lattice.hpp, LatticeCreator.cpp, LatticeCreator.hpp, |
650 |
> |
LatticeFactory.cpp, LatticeFactory.hpp, MoLocator.cpp, |
651 |
> |
MoLocator.hpp, Vector3d.hpp, cmdline.c, cmdline.h, nanoBuilder.cpp, |
652 |
> |
nanoBuilder.hpp, oopse.cpp, simpleBuilder.cpp, simpleBuilder.ggo, |
653 |
> |
simpleBuilderCmd.c, simpleBuilderCmd.h, dump2Xyz/Dump2XYZ.cpp, |
654 |
> |
dump2Xyz/Dump2XYZ.ggo, dump2Xyz/Dump2XYZCmd.c, |
655 |
> |
dump2Xyz/Dump2XYZCmd.h, dump2Xyz/Makefile, oopse/Makefile, |
656 |
> |
oopse/oopse.cpp, simpleBuilder/BaseLattice.cpp, |
657 |
> |
simpleBuilder/BaseLattice.hpp, simpleBuilder/Lattice.cpp, |
658 |
> |
simpleBuilder/Lattice.hpp, simpleBuilder/LatticeCreator.cpp, |
659 |
> |
simpleBuilder/LatticeCreator.hpp, simpleBuilder/LatticeFactory.cpp, |
660 |
> |
simpleBuilder/LatticeFactory.hpp, simpleBuilder/Make.ftemp.old, |
661 |
> |
simpleBuilder/Makefile, simpleBuilder/MoLocator.cpp, |
662 |
> |
simpleBuilder/MoLocator.hpp, simpleBuilder/Vector3d.hpp, |
663 |
> |
simpleBuilder/simpleBuilder.cpp, simpleBuilder/simpleBuilder.ggo, |
664 |
> |
simpleBuilder/simpleBuilderCmd.c, simpleBuilder/simpleBuilderCmd.h: |
665 |
> |
change directory structure of application. Every executable file is |
666 |
> |
replaced in seperate directory |
667 |
> |
|
668 |
> |
2004-09-28 17:15 gezelter |
669 |
> |
|
670 |
> |
* lib/dummy: Keep that lib around, please. |
671 |
> |
|
672 |
> |
2004-09-28 17:14 gezelter |
673 |
> |
|
674 |
> |
* Makefile, configure, ac-tools/configure.in, make/Make.conf.in: |
675 |
> |
starting a configure version |
676 |
> |
|
677 |
> |
2004-09-28 16:08 tim |
678 |
> |
|
679 |
> |
* src/: UseTheForce/Makefile, UseTheForce/notifyCutoffs.F90, |
680 |
> |
UseTheForce/DarkSide/Makefile, |
681 |
> |
UseTheForce/DarkSide/notifyCutoffs.F90, |
682 |
> |
UseTheForce/DarkSide/simulation_module.F90, brains/Makedepend, |
683 |
> |
brains/Makefile, brains/simulation_module.F90: move fortran files |
684 |
> |
around to solve dependency problem |
685 |
> |
|
686 |
> |
2004-09-28 15:43 tim |
687 |
> |
|
688 |
> |
* Makefile, src/UseTheForce/ForceFields.hpp, |
689 |
> |
src/UseTheForce/Makefile, src/applications/BaseLattice.hpp, |
690 |
> |
src/applications/Makedepend, src/applications/Makefile, |
691 |
> |
src/brains/Makedepend, src/brains/simulation_module.F90, |
692 |
> |
src/integrators/AllIntegrator.hpp, src/math/Euler3.cpp, |
693 |
> |
src/math/Makefile, src/minimizers/OOPSEMinimizer.cpp, |
694 |
> |
src/utils/Makefile: [no log message] |
695 |
> |
|
696 |
> |
2004-09-28 15:41 tim |
697 |
> |
|
698 |
> |
* make/Makefile, scripts/sfmakedepend: fix fortran dependency |
699 |
> |
problem |
700 |
> |
|
701 |
> |
2004-09-28 11:13 tim |
702 |
> |
|
703 |
> |
* make/Makefile, src/io/BASSlex.l, src/io/BASSyacc.y, |
704 |
> |
src/io/Makefile: add yacc and lex rules |
705 |
> |
|
706 |
> |
2004-09-27 15:24 tim |
707 |
> |
|
708 |
> |
* make/Makefile: adding include path to F90Options |
709 |
> |
|
710 |
> |
2004-09-27 15:13 tim |
711 |
> |
|
712 |
> |
* make/Makefile: change suffix from .cc to .cpp |
713 |
> |
|
714 |
> |
2004-09-24 11:27 tim |
715 |
> |
|
716 |
> |
* src/: UseTheForce/DUFF.cpp, UseTheForce/EAM_FF.cpp, |
717 |
> |
UseTheForce/ForceFields.cpp, UseTheForce/ForceFields.hpp, |
718 |
> |
UseTheForce/LJFF.cpp, UseTheForce/WATER.cpp, |
719 |
> |
UseTheForce/do_Forces.F90, UseTheForce/fortranWrapDefines.hpp, |
720 |
> |
UseTheForce/fortranWrappers.cpp, UseTheForce/fortranWrappers.hpp, |
721 |
> |
UseTheForce/mpiForceField.c, UseTheForce/mpiSimulation_module.F90, |
722 |
> |
UseTheForce/DarkSide/calc_LJ_FF.F90, |
723 |
> |
UseTheForce/DarkSide/notifyCutoffs.F90, |
724 |
> |
UseTheForce/DarkSide/switch_module.F90, |
725 |
> |
applications/BaseLattice.cpp, applications/Dump2XYZ.cpp, |
726 |
> |
applications/Dump2XYZCmd.c, applications/Lattice.cpp, |
727 |
> |
applications/Lattice.hpp, applications/LatticeCreator.cpp, |
728 |
> |
applications/LatticeCreator.hpp, applications/LatticeFactory.cpp, |
729 |
> |
applications/MoLocator.cpp, applications/MoLocator.hpp, |
730 |
> |
applications/cmdline.c, applications/nanoBuilder.cpp, |
731 |
> |
applications/oopse.cpp, applications/simpleBuilder.cpp, |
732 |
> |
applications/simpleBuilderCmd.c, brains/Exclude.cpp, |
733 |
> |
brains/ForceFields.cpp, brains/SimInfo.cpp, brains/SimInfo.hpp, |
734 |
> |
brains/SimSetup.cpp, brains/SimSetup.hpp, brains/SimState.cpp, |
735 |
> |
brains/SkipList.cpp, brains/Thermo.cpp, brains/Thermo.hpp, |
736 |
> |
brains/mpiSimulation.cpp, brains/mpiSimulation.hpp, |
737 |
> |
constraints/AbstractClasses.hpp, constraints/ZConstraint.cpp, |
738 |
> |
integrators/AbstractClasses.hpp, integrators/Integrator.cpp, |
739 |
> |
integrators/Integrator.hpp, integrators/NPT.cpp, |
740 |
> |
integrators/NPTf.cpp, integrators/NPTi.cpp, integrators/NPTxyz.cpp, |
741 |
> |
integrators/NVT.cpp, io/BASS_interface.cpp, io/BASS_parse.c, |
742 |
> |
io/DumpReader.cpp, io/DumpWriter.cpp, io/Globals.cpp, |
743 |
> |
io/Globals.hpp, io/InitializeFromFile.cpp, io/LinkedAssign.cpp, |
744 |
> |
io/LinkedCommand.cpp, io/ReadWrite.hpp, io/StatWriter.cpp, |
745 |
> |
io/ZConsReader.cpp, io/ZConsReader.hpp, io/ZConsWriter.cpp, |
746 |
> |
io/ZConsWriter.hpp, io/interface.c, io/make_nodes.c, |
747 |
> |
io/make_nodes.h, io/mpiBASS.c, io/mpiBASS.h, io/parse_interface.h, |
748 |
> |
io/parse_tree.c, io/parse_tree.h, math/Euler3.cpp, math/MatVec3.c, |
749 |
> |
math/MatVec3.h, math/randomSPRNG.cpp, |
750 |
> |
minimizers/CGFamilyMinimizer.cpp, minimizers/OOPSEMinimizer.cpp, |
751 |
> |
minimizers/OOPSEMinimizer.hpp, minimizers/PRCG.cpp, |
752 |
> |
minimizers/SDMinimizer.cpp, primitives/AbstractClasses.hpp, |
753 |
> |
primitives/Atom.cpp, primitives/Atom.hpp, primitives/Bend.cpp, |
754 |
> |
primitives/BendExtensions.cpp, primitives/Bond.cpp, |
755 |
> |
primitives/BondExtensions.cpp, primitives/CutoffGroup.hpp, |
756 |
> |
primitives/DirectionalAtom.cpp, primitives/DirectionalAtom.hpp, |
757 |
> |
primitives/GhostBend.cpp, primitives/Molecule.cpp, |
758 |
> |
primitives/Molecule.hpp, primitives/RigidBody.cpp, |
759 |
> |
primitives/RigidBody.hpp, primitives/SRI.hpp, |
760 |
> |
primitives/StuntDouble.cpp, primitives/StuntDouble.hpp, |
761 |
> |
primitives/Torsion.cpp, primitives/TorsionExtensions.cpp, |
762 |
> |
profiling/mdProfile.cpp, restraints/Restraints.cpp, |
763 |
> |
restraints/Restraints.hpp, types/AtomStamp.cpp, |
764 |
> |
types/AtomStamp.hpp, types/BendStamp.cpp, types/BendStamp.hpp, |
765 |
> |
types/BondStamp.cpp, types/BondStamp.hpp, types/Component.cpp, |
766 |
> |
types/CutoffGroupStamp.cpp, types/CutoffGroupStamp.hpp, |
767 |
> |
types/MakeStamps.cpp, types/MakeStamps.hpp, |
768 |
> |
types/MoleculeStamp.cpp, types/MoleculeStamp.hpp, |
769 |
> |
types/RigidBodyStamp.cpp, types/RigidBodyStamp.hpp, |
770 |
> |
types/TorsionStamp.cpp, types/TorsionStamp.hpp, |
771 |
> |
types/ZconStamp.cpp, types/ZconStamp.hpp, utils/GenericData.cpp, |
772 |
> |
utils/StreamTokenizer.cpp, utils/StringUtils.c, |
773 |
> |
utils/StringUtils.cpp, utils/Utility.cpp, utils/fError.c, |
774 |
> |
utils/simError.c, visitors/AtomVisitor.cpp, |
775 |
> |
visitors/AtomVisitor.hpp, visitors/CompositeVisitor.cpp, |
776 |
> |
visitors/CompositeVisitor.hpp, visitors/OtherVisitor.cpp, |
777 |
> |
visitors/OtherVisitor.hpp, visitors/RigidBodyVisitor.cpp, |
778 |
> |
visitors/RigidBodyVisitor.hpp, visitors/ZconsVisitor.cpp, |
779 |
> |
visitors/ZconsVisitor.hpp: change the #include in source files |
780 |
> |
|
781 |
> |
2004-09-23 23:16 gezelter |
782 |
> |
|
783 |
> |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
784 |
> |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
785 |
> |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
786 |
> |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
787 |
> |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
788 |
> |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
789 |
> |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
790 |
> |
src/UseTheForce/fForceField.h, |
791 |
> |
src/UseTheForce/fSwitchingFunction.h, |
792 |
> |
src/UseTheForce/fortranWrapDefines.hpp, |
793 |
> |
src/UseTheForce/fortranWrappers.cpp, |
794 |
> |
src/UseTheForce/fortranWrappers.hpp, |
795 |
> |
src/UseTheForce/mpiComponentPlan.h, |
796 |
> |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
797 |
> |
src/UseTheForce/mpiSimulation_module.F90, |
798 |
> |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
799 |
> |
src/UseTheForce/DarkSide/atype_module.F90, |
800 |
> |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
801 |
> |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
802 |
> |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
803 |
> |
src/UseTheForce/DarkSide/calc_eam.F90, |
804 |
> |
src/UseTheForce/DarkSide/calc_gb.F90, |
805 |
> |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
806 |
> |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
807 |
> |
src/UseTheForce/DarkSide/force_globals.F90, |
808 |
> |
src/UseTheForce/DarkSide/neighborLists.F90, |
809 |
> |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
810 |
> |
src/UseTheForce/DarkSide/switch_module.F90, |
811 |
> |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
812 |
> |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
813 |
> |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
814 |
> |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
815 |
> |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
816 |
> |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
817 |
> |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
818 |
> |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
819 |
> |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
820 |
> |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
821 |
> |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
822 |
> |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
823 |
> |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
824 |
> |
src/types/BondStamp.hpp, src/types/Component.cpp, |
825 |
> |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
826 |
> |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
827 |
> |
src/types/MakeStamps.hpp, src/types/Makefile, |
828 |
> |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
829 |
> |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
830 |
> |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
831 |
> |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
832 |
> |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
833 |
> |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
834 |
> |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
835 |
> |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
836 |
> |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
837 |
> |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
838 |
> |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
839 |
> |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
840 |
> |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
841 |
> |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
842 |
> |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
843 |
> |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
844 |
> |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
845 |
> |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
846 |
> |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
847 |
> |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
848 |
> |
src/minimizers/OOPSEMinimizer.cpp, |
849 |
> |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
850 |
> |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
851 |
> |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
852 |
> |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
853 |
> |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
854 |
> |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
855 |
> |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
856 |
> |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
857 |
> |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
858 |
> |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
859 |
> |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
860 |
> |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
861 |
> |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
862 |
> |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
863 |
> |
src/utils/GenericData.hpp, src/utils/Makefile, |
864 |
> |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
865 |
> |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
866 |
> |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
867 |
> |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
868 |
> |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
869 |
> |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
870 |
> |
src/utils/simError.c, src/utils/simError.h, |
871 |
> |
src/utils/status_module.F90, src/utils/vector_class.F90, |
872 |
> |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
873 |
> |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
874 |
> |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
875 |
> |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
876 |
> |
src/visitors/RigidBodyVisitor.cpp, |
877 |
> |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
878 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
879 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
880 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
881 |
> |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
882 |
> |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
883 |
> |
samples/zcons/Makefile.in, samples/zcons/water.md, |
884 |
> |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
885 |
> |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
886 |
> |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
887 |
> |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
888 |
> |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
889 |
> |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
890 |
> |
src/applications/LatticeCreator.cpp, |
891 |
> |
src/applications/LatticeCreator.hpp, |
892 |
> |
src/applications/LatticeFactory.cpp, |
893 |
> |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
894 |
> |
src/applications/Makefile, src/applications/MoLocator.cpp, |
895 |
> |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
896 |
> |
src/applications/cmdline.c, src/applications/cmdline.h, |
897 |
> |
src/applications/getopt.c, src/applications/getopt1.c, |
898 |
> |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
899 |
> |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
900 |
> |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
901 |
> |
src/applications/simpleBuilder.ggo, |
902 |
> |
src/applications/simpleBuilderCmd.c, |
903 |
> |
src/integrators/AbstractClasses.hpp, |
904 |
> |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
905 |
> |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
906 |
> |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
907 |
> |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
908 |
> |
src/integrators/NVT.cpp, src/profiling/Makefile, |
909 |
> |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
910 |
> |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
911 |
> |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
912 |
> |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
913 |
> |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
914 |
> |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
915 |
> |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
916 |
> |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
917 |
> |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
918 |
> |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
919 |
> |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
920 |
> |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
921 |
> |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
922 |
> |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
923 |
> |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
924 |
> |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
925 |
> |
samples/alkane/butane.in, samples/alkane/butane.md, |
926 |
> |
samples/argon/500.in, samples/argon/500.md, |
927 |
> |
samples/argon/Makefile.in, samples/argon/ar864.in, |
928 |
> |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
929 |
> |
samples/argon/argonNVT.md, samples/argon/lj.md, |
930 |
> |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
931 |
> |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
932 |
> |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
933 |
> |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
934 |
> |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
935 |
> |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
936 |
> |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
937 |
> |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
938 |
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
939 |
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
940 |
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
941 |
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
942 |
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
943 |
< |
forceFields/LJFF.frc, forceFields/Makefile, |
944 |
< |
forceFields/Makefile.in, forceFields/Ni.VC.funcfl, |
945 |
< |
forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl, |
946 |
< |
forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl, |
947 |
< |
forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl, |
948 |
< |
forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl, |
949 |
< |
forceFields/WATER.frc, libBASS/AtomStamp.cpp, |
950 |
< |
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
951 |
< |
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
952 |
< |
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
953 |
< |
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
954 |
< |
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
357 |
< |
libBASS/Component.cpp, libBASS/Component.hpp, |
358 |
< |
libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp, |
359 |
< |
libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
360 |
< |
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
361 |
< |
libBASS/LinkedCommand.hpp, libBASS/Make.dep, |
362 |
< |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
363 |
< |
libBASS/Makefile.in, libBASS/MoleculeStamp.cpp, |
364 |
< |
libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp, |
365 |
< |
libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp, |
366 |
< |
libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp, |
367 |
< |
libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c, |
368 |
< |
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
369 |
< |
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
370 |
< |
libBASS/parse_interface.h, libBASS/parse_me.h, |
371 |
< |
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
372 |
< |
libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy, |
373 |
< |
libBASS/obj/dummy, libmdtools/AbstractClasses.hpp, |
374 |
< |
libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp, |
375 |
< |
libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp, |
376 |
< |
libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp, |
377 |
< |
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
378 |
< |
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
379 |
< |
libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp, |
380 |
< |
libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp, |
381 |
< |
libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp, |
382 |
< |
libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp, |
383 |
< |
libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp, |
384 |
< |
libmdtools/Euler3.cpp, libmdtools/Euler3.hpp, |
385 |
< |
libmdtools/Exclude.cpp, libmdtools/Exclude.hpp, |
386 |
< |
libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp, |
387 |
< |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
388 |
< |
libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp, |
389 |
< |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
390 |
< |
libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile, |
391 |
< |
libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h, |
392 |
< |
libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp, |
393 |
< |
libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
394 |
< |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
395 |
< |
libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, |
396 |
< |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
397 |
< |
libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp, |
398 |
< |
libmdtools/Restraints.cpp, libmdtools/Restraints.hpp, |
399 |
< |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
400 |
< |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
401 |
< |
libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp, |
402 |
< |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
403 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
404 |
< |
libmdtools/SimState.cpp, libmdtools/SimState.hpp, |
405 |
< |
libmdtools/SkipList.cpp, libmdtools/SkipList.hpp, |
406 |
< |
libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp, |
407 |
< |
libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c, |
408 |
< |
libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp, |
409 |
< |
libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp, |
410 |
< |
libmdtools/Thermo.hpp, libmdtools/Torsion.cpp, |
411 |
< |
libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp, |
412 |
< |
libmdtools/Utility.cpp, libmdtools/Utility.hpp, |
413 |
< |
libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp, |
414 |
< |
libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp, |
415 |
< |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp, |
416 |
< |
libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp, |
417 |
< |
libmdtools/atype_module.F90, libmdtools/calc_LJ_FF.F90, |
418 |
< |
libmdtools/calc_charge_charge.F90, |
419 |
< |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
420 |
< |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
421 |
< |
libmdtools/calc_sticky_pair.F90, libmdtools/config.h.in, |
422 |
< |
libmdtools/definitions_module.F90, libmdtools/do_Forces.F90, |
423 |
< |
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
424 |
< |
libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp, |
425 |
< |
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
426 |
< |
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
427 |
< |
libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp, |
428 |
< |
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
429 |
< |
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
430 |
< |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
431 |
< |
libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90, |
432 |
< |
libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp, |
433 |
< |
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
434 |
< |
libmdtools/status_module.F90, libmdtools/switch_module.F90, |
435 |
< |
libmdtools/timing.F90, libmdtools/vector_class.F90, |
436 |
< |
libmdtools/wrappers.F90, libmdtools/MPIobj/dummy, |
437 |
< |
libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in, |
438 |
< |
samples/alkane/Makefile, samples/alkane/Makefile.in, |
439 |
< |
samples/alkane/alkanes.mdl, samples/alkane/butane.bass, |
440 |
< |
samples/alkane/butane.eor, samples/alkane/init_butane.eor, |
441 |
< |
samples/argon/500.bass, samples/argon/500.eor, |
442 |
< |
samples/argon/500.in, samples/argon/Makefile, |
443 |
< |
samples/argon/Makefile.in, samples/argon/NVT.bass, |
444 |
< |
samples/argon/ar864.bass, samples/argon/ar864.eor, |
445 |
< |
samples/argon/ar864.in, samples/argon/argon.bass, |
446 |
< |
samples/argon/argon.eor, samples/argon/argonEM.bass, |
447 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
448 |
< |
samples/argon/machines, samples/lipid/5x5.bass, |
449 |
< |
samples/lipid/5x5.eor, samples/lipid/Makefile, |
450 |
< |
samples/lipid/Makefile.in, samples/lipid/init_5x5.eor, |
451 |
< |
samples/lipid/lipid.mdl, samples/lipid/water.mdl, |
452 |
< |
samples/metals/Au.bass, samples/metals/Au.eor, |
453 |
< |
samples/metals/Makefile, samples/metals/Makefile.in, |
454 |
< |
samples/metals/init_au.in, samples/metals/metals.mdl, |
455 |
< |
samples/water/200.in, samples/water/Makefile, |
456 |
< |
samples/water/Makefile.in, samples/water/init_ssd.eor, |
457 |
< |
samples/water/spce.bass, samples/water/spce.eor, |
458 |
< |
samples/water/ssd.bass, samples/water/ssd.eor, |
459 |
< |
samples/water/tim.bass, samples/water/tim.eor, |
460 |
< |
samples/water/tim.init, samples/water/tim.xyz, |
461 |
< |
samples/water/tip3p.bass, samples/water/tip3p.eor, |
462 |
< |
samples/water/tip3p.init, samples/water/two.bass, |
463 |
< |
samples/water/two.eor, samples/water/two.init, |
464 |
< |
samples/water/two.xyz, samples/water/water.mdl, |
465 |
< |
samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass, |
466 |
< |
samples/water/spce/water.mdl, samples/water/ssde/256init.in, |
467 |
< |
samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl, |
468 |
< |
samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass, |
469 |
< |
samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl, |
470 |
< |
scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in, |
471 |
< |
src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy, |
472 |
< |
third-party/Makefile, third-party/Makefile.in, |
473 |
< |
third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, |
474 |
< |
utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep, |
475 |
< |
utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub, |
476 |
< |
utils/MPIobj/placeHolder, utils/obj/placeHolder, |
477 |
< |
utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile, |
478 |
< |
utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp, |
479 |
< |
utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c, |
480 |
< |
utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp, |
481 |
< |
utils/sysbuilder/latticeBuilder.cpp, |
482 |
< |
utils/sysbuilder/latticeBuilder.hpp, |
483 |
< |
utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp, |
484 |
< |
utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp, |
485 |
< |
utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp, |
486 |
< |
utils/sysbuilder/MPIobj/placeHolder, |
487 |
< |
utils/sysbuilder/obj/placeHolder: Initial import of OOPSE-1.0 |
488 |
< |
source tree |
943 |
> |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
944 |
> |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
945 |
> |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
946 |
> |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
947 |
> |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
948 |
> |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
949 |
> |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
950 |
> |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
951 |
> |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
952 |
> |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
953 |
> |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
954 |
> |
forceFields/Pt.VC.funcfl: Import of OOPSE v. 2.0 |
955 |
|
|
956 |
< |
2004-07-16 13:57 gezelter |
956 |
> |
2004-09-23 23:16 gezelter |
957 |
|
|
958 |
< |
* AUTHORS, ChangeLog, LICENSE, Makefile, Makefile.in, NEWS, README, |
959 |
< |
configure, ac-tools/Make.conf.in, ac-tools/aclocal.m4, |
960 |
< |
ac-tools/config.guess, ac-tools/config.sub, ac-tools/configure.in, |
961 |
< |
ac-tools/fortran90.m4, ac-tools/install-sh, ac-tools/shtool, |
962 |
< |
forceFields/Ag.VC.funcfl, forceFields/Ag.u3.funcfl, |
963 |
< |
forceFields/Ag.u6.funcfl, forceFields/Al.VC.funcfl, |
964 |
< |
forceFields/Au.VC.funcfl, forceFields/Au.u3.funcfl, |
958 |
> |
* AUTHORS, ChangeLog, LICENSE, Makefile, README, configure, |
959 |
> |
src/Makefile, src/config.h.in, src/constraints/AbstractClasses.hpp, |
960 |
> |
src/constraints/Makefile, src/constraints/ZConstraint.cpp, |
961 |
> |
src/UseTheForce/DUFF.cpp, src/UseTheForce/EAM_FF.cpp, |
962 |
> |
src/UseTheForce/ForceFields.cpp, src/UseTheForce/ForceFields.hpp, |
963 |
> |
src/UseTheForce/LJFF.cpp, src/UseTheForce/Makefile, |
964 |
> |
src/UseTheForce/WATER.cpp, src/UseTheForce/do_Forces.F90, |
965 |
> |
src/UseTheForce/fForceField.h, |
966 |
> |
src/UseTheForce/fSwitchingFunction.h, |
967 |
> |
src/UseTheForce/fortranWrapDefines.hpp, |
968 |
> |
src/UseTheForce/fortranWrappers.cpp, |
969 |
> |
src/UseTheForce/fortranWrappers.hpp, |
970 |
> |
src/UseTheForce/mpiComponentPlan.h, |
971 |
> |
src/UseTheForce/mpiForceField.c, src/UseTheForce/mpiForceField.h, |
972 |
> |
src/UseTheForce/mpiSimulation_module.F90, |
973 |
> |
src/UseTheForce/wrappers.F90, src/UseTheForce/DarkSide/Makefile, |
974 |
> |
src/UseTheForce/DarkSide/atype_module.F90, |
975 |
> |
src/UseTheForce/DarkSide/calc_LJ_FF.F90, |
976 |
> |
src/UseTheForce/DarkSide/calc_charge_charge.F90, |
977 |
> |
src/UseTheForce/DarkSide/calc_dipole_dipole.F90, |
978 |
> |
src/UseTheForce/DarkSide/calc_eam.F90, |
979 |
> |
src/UseTheForce/DarkSide/calc_gb.F90, |
980 |
> |
src/UseTheForce/DarkSide/calc_reaction_field.F90, |
981 |
> |
src/UseTheForce/DarkSide/calc_sticky_pair.F90, |
982 |
> |
src/UseTheForce/DarkSide/force_globals.F90, |
983 |
> |
src/UseTheForce/DarkSide/neighborLists.F90, |
984 |
> |
src/UseTheForce/DarkSide/notifyCutoffs.F90, |
985 |
> |
src/UseTheForce/DarkSide/switch_module.F90, |
986 |
> |
src/io/BASS_interface.h, src/io/BASS_parse.c, src/io/BASS_parse.h, |
987 |
> |
src/io/BASSlex.l, src/io/BASSyacc.y, src/io/DumpReader.cpp, |
988 |
> |
src/io/DumpWriter.cpp, src/io/Globals.cpp, |
989 |
> |
src/io/InitializeFromFile.cpp, src/io/LinkedAssign.hpp, |
990 |
> |
src/io/LinkedCommand.cpp, src/io/LinkedCommand.hpp, |
991 |
> |
src/io/Makefile, src/io/ReadWrite.hpp, src/io/StatWriter.cpp, |
992 |
> |
src/io/ZConsReader.hpp, src/io/ZConsWriter.cpp, |
993 |
> |
src/io/ZConsWriter.hpp, src/io/interface.c, src/io/make_nodes.c, |
994 |
> |
src/io/make_nodes.h, src/io/mpiBASS.c, src/io/mpiBASS.h, |
995 |
> |
src/io/node_list.h, src/io/parse_interface.h, src/io/parse_me.h, |
996 |
> |
src/io/parse_tree.c, src/io/parse_tree.h, src/types/AtomStamp.cpp, |
997 |
> |
src/types/AtomStamp.hpp, src/types/BendStamp.cpp, |
998 |
> |
src/types/BendStamp.hpp, src/types/BondStamp.cpp, |
999 |
> |
src/types/BondStamp.hpp, src/types/Component.cpp, |
1000 |
> |
src/types/Component.hpp, src/types/CutoffGroupStamp.cpp, |
1001 |
> |
src/types/CutoffGroupStamp.hpp, src/types/MakeStamps.cpp, |
1002 |
> |
src/types/MakeStamps.hpp, src/types/Makefile, |
1003 |
> |
src/types/MoleculeStamp.cpp, src/types/MoleculeStamp.hpp, |
1004 |
> |
src/types/RigidBodyStamp.cpp, src/types/RigidBodyStamp.hpp, |
1005 |
> |
src/types/TorsionStamp.cpp, src/types/TorsionStamp.hpp, |
1006 |
> |
src/types/ZconStamp.cpp, src/types/ZconStamp.hpp, |
1007 |
> |
src/applications/simpleBuilderCmd.h, src/brains/Exclude.cpp, |
1008 |
> |
src/brains/Exclude.hpp, src/brains/ForceFields.cpp, |
1009 |
> |
src/brains/Makedepend, src/brains/Makefile, src/brains/SimInfo.cpp, |
1010 |
> |
src/brains/SimInfo.hpp, src/brains/SimSetup.cpp, |
1011 |
> |
src/brains/SimSetup.hpp, src/brains/SimState.cpp, |
1012 |
> |
src/brains/SimState.hpp, src/brains/SkipList.cpp, |
1013 |
> |
src/brains/SkipList.hpp, src/brains/Thermo.cpp, |
1014 |
> |
src/brains/Thermo.hpp, src/brains/fSimulation.h, |
1015 |
> |
src/brains/mpiSimulation.cpp, src/brains/mpiSimulation.hpp, |
1016 |
> |
src/brains/simulation_module.F90, src/io/BASS_interface.cpp, |
1017 |
> |
src/io/Globals.hpp, src/io/LinkedAssign.cpp, |
1018 |
> |
src/io/ZConsReader.cpp, src/math/Euler3.cpp, src/math/Euler3.hpp, |
1019 |
> |
src/math/Makefile, src/math/MatVec3.c, src/math/MatVec3.h, |
1020 |
> |
src/math/mt19937ar.c, src/math/randomSPRNG.cpp, |
1021 |
> |
src/math/randomSPRNG.hpp, src/minimizers/CGFamilyMinimizer.cpp, |
1022 |
> |
src/minimizers/Makefile, src/minimizers/MinimizerParameterSet.hpp, |
1023 |
> |
src/minimizers/OOPSEMinimizer.cpp, |
1024 |
> |
src/minimizers/OOPSEMinimizer.hpp, src/minimizers/PRCG.cpp, |
1025 |
> |
src/minimizers/SDMinimizer.cpp, src/primitives/AbstractClasses.hpp, |
1026 |
> |
src/primitives/Atom.cpp, src/primitives/Atom.hpp, |
1027 |
> |
src/primitives/Bend.cpp, src/primitives/BendExtensions.cpp, |
1028 |
> |
src/primitives/Bond.cpp, src/primitives/BondExtensions.cpp, |
1029 |
> |
src/primitives/CutoffGroup.hpp, src/primitives/DirectionalAtom.cpp, |
1030 |
> |
src/primitives/DirectionalAtom.hpp, src/primitives/GhostBend.cpp, |
1031 |
> |
src/primitives/Makefile, src/primitives/Molecule.cpp, |
1032 |
> |
src/primitives/Molecule.hpp, src/primitives/RigidBody.cpp, |
1033 |
> |
src/primitives/RigidBody.hpp, src/primitives/SRI.hpp, |
1034 |
> |
src/primitives/StuntDouble.cpp, src/primitives/StuntDouble.hpp, |
1035 |
> |
src/primitives/Torsion.cpp, src/primitives/TorsionExtensions.cpp, |
1036 |
> |
src/restraints/Makefile, src/restraints/Restraints.cpp, |
1037 |
> |
src/restraints/Restraints.hpp, src/utils/GenericData.cpp, |
1038 |
> |
src/utils/GenericData.hpp, src/utils/Makefile, |
1039 |
> |
src/utils/StreamTokenizer.cpp, src/utils/StreamTokenizer.hpp, |
1040 |
> |
src/utils/StringUtils.c, src/utils/StringUtils.cpp, |
1041 |
> |
src/utils/StringUtils.h, src/utils/StringUtils.hpp, |
1042 |
> |
src/utils/TypeInfo.hpp, src/utils/Utility.cpp, |
1043 |
> |
src/utils/Utility.hpp, src/utils/definitions_module.F90, |
1044 |
> |
src/utils/fError.c, src/utils/oopseMPI_module.F90, |
1045 |
> |
src/utils/simError.c, src/utils/simError.h, |
1046 |
> |
src/utils/status_module.F90, src/utils/vector_class.F90, |
1047 |
> |
src/visitors/AtomVisitor.cpp, src/visitors/AtomVisitor.hpp, |
1048 |
> |
src/visitors/BaseVisitor.hpp, src/visitors/CompositeVisitor.cpp, |
1049 |
> |
src/visitors/CompositeVisitor.hpp, src/visitors/Makefile, |
1050 |
> |
src/visitors/OtherVisitor.cpp, src/visitors/OtherVisitor.hpp, |
1051 |
> |
src/visitors/RigidBodyVisitor.cpp, |
1052 |
> |
src/visitors/RigidBodyVisitor.hpp, src/visitors/ZconsVisitor.cpp, |
1053 |
> |
src/visitors/ZconsVisitor.hpp, make/Makefile, samples/Makefile.in, |
1054 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.in, |
1055 |
> |
samples/metals/Au-Core-Ag-Shell_Nanoparticle.md, |
1056 |
> |
samples/metals/Au_bulk_FBD.md, samples/metals/Au_bulk_voter.md, |
1057 |
> |
samples/metals/Au_nanoparticle.md, samples/metals/Makefile.in, |
1058 |
> |
samples/zcons/Makefile.in, samples/zcons/water.md, |
1059 |
> |
samples/zcons/zconsFixed.in, samples/zcons/zconsFixed.md, |
1060 |
> |
samples/zcons/zconsMoving.in, samples/zcons/zconsMoving.md, |
1061 |
> |
src/applications/BaseLattice.cpp, src/applications/BaseLattice.hpp, |
1062 |
> |
src/applications/Dump2XYZ.cpp, src/applications/Dump2XYZ.ggo, |
1063 |
> |
src/applications/Dump2XYZCmd.c, src/applications/Dump2XYZCmd.h, |
1064 |
> |
src/applications/Lattice.cpp, src/applications/Lattice.hpp, |
1065 |
> |
src/applications/LatticeCreator.cpp, |
1066 |
> |
src/applications/LatticeCreator.hpp, |
1067 |
> |
src/applications/LatticeFactory.cpp, |
1068 |
> |
src/applications/LatticeFactory.hpp, src/applications/Makedepend, |
1069 |
> |
src/applications/Makefile, src/applications/MoLocator.cpp, |
1070 |
> |
src/applications/MoLocator.hpp, src/applications/Vector3d.hpp, |
1071 |
> |
src/applications/cmdline.c, src/applications/cmdline.h, |
1072 |
> |
src/applications/getopt.c, src/applications/getopt1.c, |
1073 |
> |
src/applications/gnugetopt.h, src/applications/nanoBuilder.cpp, |
1074 |
> |
src/applications/nanoBuilder.hpp, src/applications/oopse.cpp, |
1075 |
> |
src/applications/quickLate.c, src/applications/simpleBuilder.cpp, |
1076 |
> |
src/applications/simpleBuilder.ggo, |
1077 |
> |
src/applications/simpleBuilderCmd.c, |
1078 |
> |
src/integrators/AbstractClasses.hpp, |
1079 |
> |
src/integrators/AllIntegrator.hpp, src/integrators/Integrator.cpp, |
1080 |
> |
src/integrators/Integrator.hpp, src/integrators/Makefile, |
1081 |
> |
src/integrators/NPT.cpp, src/integrators/NPTf.cpp, |
1082 |
> |
src/integrators/NPTi.cpp, src/integrators/NPTxyz.cpp, |
1083 |
> |
src/integrators/NVT.cpp, src/profiling/Makefile, |
1084 |
> |
src/profiling/mdProfile.cpp, src/profiling/mdProfile.hpp, |
1085 |
> |
src/profiling/timing.F90, samples/metals/Au_bulk.in, |
1086 |
> |
samples/metals/Au_nanoparticle.in, samples/metals/metals.md, |
1087 |
> |
samples/water/Makefile.in, samples/water/dimer/Makefile.in, |
1088 |
> |
samples/water/dimer/two.in, samples/water/dimer/two.md, |
1089 |
> |
samples/water/dimer/water.md, samples/water/spce/Makefile.in, |
1090 |
> |
samples/water/spce/spce.in, samples/water/spce/spce.md, |
1091 |
> |
samples/water/spce/water.md, samples/water/ssde/Makefile.in, |
1092 |
> |
samples/water/ssde/ssde.in, samples/water/ssde/ssde.md, |
1093 |
> |
samples/water/ssde/water.md, samples/water/tip3p_ice/Makefile.in, |
1094 |
> |
samples/water/tip3p_ice/tp3.in, samples/water/tip3p_ice/tp3.md, |
1095 |
> |
samples/water/tip3p_ice/water.md, samples/water/ssd/Makefile.in, |
1096 |
> |
samples/water/ssd/ssd.in, samples/water/ssd/ssd.md, |
1097 |
> |
samples/water/ssd/water.md, samples/water/tip4p/tp4.in, |
1098 |
> |
samples/water/tip4p/tp4.md, samples/water/tip4p/water.md, |
1099 |
> |
samples/alkane/Makefile.in, samples/alkane/alkanes.md, |
1100 |
> |
samples/alkane/butane.in, samples/alkane/butane.md, |
1101 |
> |
samples/argon/500.in, samples/argon/500.md, |
1102 |
> |
samples/argon/Makefile.in, samples/argon/ar864.in, |
1103 |
> |
samples/argon/ar864.md, samples/argon/argonNVT.in, |
1104 |
> |
samples/argon/argonNVT.md, samples/argon/lj.md, |
1105 |
> |
samples/lipid/5x5.in, samples/lipid/5x5.md, |
1106 |
> |
samples/lipid/Makefile.in, samples/lipid/lipid.md, |
1107 |
> |
samples/lipid/water.md, samples/minimizer/Makefile.in, |
1108 |
> |
samples/minimizer/WATER.frc, samples/minimizer/ssdEM.in, |
1109 |
> |
samples/minimizer/ssdEM.md, samples/minimizer/tip4p_two.in, |
1110 |
> |
samples/minimizer/tip4p_two.md, samples/minimizer/water.md, |
1111 |
> |
samples/water/tip4p/Makefile.in, forceFields/Ag.VC.funcfl, |
1112 |
> |
forceFields/Ag.u3.funcfl, forceFields/Ag.u6.funcfl, |
1113 |
|
forceFields/Au.u6.funcfl, forceFields/Cu.VC.funcfl, |
1114 |
|
forceFields/Cu.u3.funcfl, forceFields/Cu.u6.funcfl, |
1115 |
|
forceFields/DUFF.frc, forceFields/DipoleTest.frc, |
1116 |
|
forceFields/EAM.VC.frc, forceFields/EAM.frc, |
1117 |
|
forceFields/EAM.u3.frc, forceFields/EAM.u6.frc, |
1118 |
< |
forceFields/LJFF.frc, forceFields/Makefile, |
1119 |
< |
forceFields/Makefile.in, forceFields/Ni.VC.funcfl, |
1120 |
< |
forceFields/Ni.u3.funcfl, forceFields/Ni.u6.funcfl, |
1121 |
< |
forceFields/Pd.VC.funcfl, forceFields/Pd.u3.funcfl, |
1122 |
< |
forceFields/Pd.u6.funcfl, forceFields/Pt.VC.funcfl, |
1123 |
< |
forceFields/Pt.u3.funcfl, forceFields/Pt.u6.funcfl, |
1124 |
< |
forceFields/WATER.frc, libBASS/AtomStamp.cpp, |
1125 |
< |
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
1126 |
< |
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
1127 |
< |
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
1128 |
< |
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
1129 |
< |
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
516 |
< |
libBASS/Component.cpp, libBASS/Component.hpp, |
517 |
< |
libBASS/CutoffGroupStamp.cpp, libBASS/CutoffGroupStamp.hpp, |
518 |
< |
libBASS/Globals.cpp, libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
519 |
< |
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
520 |
< |
libBASS/LinkedCommand.hpp, libBASS/Make.dep, |
521 |
< |
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
522 |
< |
libBASS/Makefile.in, libBASS/MoleculeStamp.cpp, |
523 |
< |
libBASS/MoleculeStamp.hpp, libBASS/RigidBodyStamp.cpp, |
524 |
< |
libBASS/RigidBodyStamp.hpp, libBASS/TorsionStamp.cpp, |
525 |
< |
libBASS/TorsionStamp.hpp, libBASS/ZconStamp.cpp, |
526 |
< |
libBASS/ZconStamp.hpp, libBASS/config.h.in, libBASS/fError.c, |
527 |
< |
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
528 |
< |
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
529 |
< |
libBASS/parse_interface.h, libBASS/parse_me.h, |
530 |
< |
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
531 |
< |
libBASS/simError.h, libBASS/y.tab.h, libBASS/MPIobj/dummy, |
532 |
< |
libBASS/obj/dummy, libmdtools/AbstractClasses.hpp, |
533 |
< |
libmdtools/AllIntegrator.hpp, libmdtools/Atom.cpp, |
534 |
< |
libmdtools/Atom.hpp, libmdtools/AtomVisitor.cpp, |
535 |
< |
libmdtools/AtomVisitor.hpp, libmdtools/BaseVisitor.hpp, |
536 |
< |
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
537 |
< |
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
538 |
< |
libmdtools/CGFamilyMinimizer.cpp, libmdtools/CompositeVisitor.cpp, |
539 |
< |
libmdtools/CompositeVisitor.hpp, libmdtools/CutoffGroup.hpp, |
540 |
< |
libmdtools/DUFF.cpp, libmdtools/DirectionalAtom.cpp, |
541 |
< |
libmdtools/DirectionalAtom.hpp, libmdtools/DumpReader.cpp, |
542 |
< |
libmdtools/DumpWriter.cpp, libmdtools/EAM_FF.cpp, |
543 |
< |
libmdtools/Euler3.cpp, libmdtools/Euler3.hpp, |
544 |
< |
libmdtools/Exclude.cpp, libmdtools/Exclude.hpp, |
545 |
< |
libmdtools/ForceFields.cpp, libmdtools/ForceFields.hpp, |
546 |
< |
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
547 |
< |
libmdtools/GhostBend.cpp, libmdtools/InitializeFromFile.cpp, |
548 |
< |
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
549 |
< |
libmdtools/LJFF.cpp, libmdtools/Make.dep, libmdtools/Makefile, |
550 |
< |
libmdtools/Makefile.in, libmdtools/MatVec3.c, libmdtools/MatVec3.h, |
551 |
< |
libmdtools/MinimizerParameterSet.hpp, libmdtools/Molecule.cpp, |
552 |
< |
libmdtools/Molecule.hpp, libmdtools/NPT.cpp, libmdtools/NPTf.cpp, |
553 |
< |
libmdtools/NPTi.cpp, libmdtools/NPTxyz.cpp, libmdtools/NVT.cpp, |
554 |
< |
libmdtools/OOPSEMinimizer.cpp, libmdtools/OOPSEMinimizer.hpp, |
555 |
< |
libmdtools/OtherVisitor.cpp, libmdtools/OtherVisitor.hpp, |
556 |
< |
libmdtools/PRCG.cpp, libmdtools/ReadWrite.hpp, |
557 |
< |
libmdtools/Restraints.cpp, libmdtools/Restraints.hpp, |
558 |
< |
libmdtools/RigidBody.cpp, libmdtools/RigidBody.hpp, |
559 |
< |
libmdtools/RigidBodyVisitor.cpp, libmdtools/RigidBodyVisitor.hpp, |
560 |
< |
libmdtools/SDMinimizer.cpp, libmdtools/SRI.hpp, |
561 |
< |
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
562 |
< |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
563 |
< |
libmdtools/SimState.cpp, libmdtools/SimState.hpp, |
564 |
< |
libmdtools/SkipList.cpp, libmdtools/SkipList.hpp, |
565 |
< |
libmdtools/StatWriter.cpp, libmdtools/StreamTokenizer.cpp, |
566 |
< |
libmdtools/StreamTokenizer.hpp, libmdtools/StringUtils.c, |
567 |
< |
libmdtools/StringUtils.h, libmdtools/StuntDouble.cpp, |
568 |
< |
libmdtools/StuntDouble.hpp, libmdtools/Thermo.cpp, |
569 |
< |
libmdtools/Thermo.hpp, libmdtools/Torsion.cpp, |
570 |
< |
libmdtools/TorsionExtensions.cpp, libmdtools/TypeInfo.hpp, |
571 |
< |
libmdtools/Utility.cpp, libmdtools/Utility.hpp, |
572 |
< |
libmdtools/WATER.cpp, libmdtools/ZConsReader.cpp, |
573 |
< |
libmdtools/ZConsReader.hpp, libmdtools/ZConsWriter.cpp, |
574 |
< |
libmdtools/ZConsWriter.hpp, libmdtools/ZConstraint.cpp, |
575 |
< |
libmdtools/ZconsVisitor.cpp, libmdtools/ZconsVisitor.hpp, |
576 |
< |
libmdtools/atype_module.F90, libmdtools/calc_LJ_FF.F90, |
577 |
< |
libmdtools/calc_charge_charge.F90, |
578 |
< |
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_eam.F90, |
579 |
< |
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
580 |
< |
libmdtools/calc_sticky_pair.F90, libmdtools/config.h.in, |
581 |
< |
libmdtools/definitions_module.F90, libmdtools/do_Forces.F90, |
582 |
< |
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
583 |
< |
libmdtools/fSwitchingFunction.h, libmdtools/forceFactory.hpp, |
584 |
< |
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
585 |
< |
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
586 |
< |
libmdtools/mdProfile.cpp, libmdtools/mdProfile.hpp, |
587 |
< |
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
588 |
< |
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
589 |
< |
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
590 |
< |
libmdtools/neighborLists.F90, libmdtools/notifyCutoffs.F90, |
591 |
< |
libmdtools/oopseMPI_module.F90, libmdtools/randomSPRNG.cpp, |
592 |
< |
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
593 |
< |
libmdtools/status_module.F90, libmdtools/switch_module.F90, |
594 |
< |
libmdtools/timing.F90, libmdtools/vector_class.F90, |
595 |
< |
libmdtools/wrappers.F90, libmdtools/MPIobj/dummy, |
596 |
< |
libmdtools/obj/dummy, samples/Makefile, samples/Makefile.in, |
597 |
< |
samples/alkane/Makefile, samples/alkane/Makefile.in, |
598 |
< |
samples/alkane/alkanes.mdl, samples/alkane/butane.bass, |
599 |
< |
samples/alkane/butane.eor, samples/alkane/init_butane.eor, |
600 |
< |
samples/argon/500.bass, samples/argon/500.eor, |
601 |
< |
samples/argon/500.in, samples/argon/Makefile, |
602 |
< |
samples/argon/Makefile.in, samples/argon/NVT.bass, |
603 |
< |
samples/argon/ar864.bass, samples/argon/ar864.eor, |
604 |
< |
samples/argon/ar864.in, samples/argon/argon.bass, |
605 |
< |
samples/argon/argon.eor, samples/argon/argonEM.bass, |
606 |
< |
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
607 |
< |
samples/argon/machines, samples/lipid/5x5.bass, |
608 |
< |
samples/lipid/5x5.eor, samples/lipid/Makefile, |
609 |
< |
samples/lipid/Makefile.in, samples/lipid/init_5x5.eor, |
610 |
< |
samples/lipid/lipid.mdl, samples/lipid/water.mdl, |
611 |
< |
samples/metals/Au.bass, samples/metals/Au.eor, |
612 |
< |
samples/metals/Makefile, samples/metals/Makefile.in, |
613 |
< |
samples/metals/init_au.in, samples/metals/metals.mdl, |
614 |
< |
samples/water/200.in, samples/water/Makefile, |
615 |
< |
samples/water/Makefile.in, samples/water/init_ssd.eor, |
616 |
< |
samples/water/spce.bass, samples/water/spce.eor, |
617 |
< |
samples/water/ssd.bass, samples/water/ssd.eor, |
618 |
< |
samples/water/tim.bass, samples/water/tim.eor, |
619 |
< |
samples/water/tim.init, samples/water/tim.xyz, |
620 |
< |
samples/water/tip3p.bass, samples/water/tip3p.eor, |
621 |
< |
samples/water/tip3p.init, samples/water/two.bass, |
622 |
< |
samples/water/two.eor, samples/water/two.init, |
623 |
< |
samples/water/two.xyz, samples/water/water.mdl, |
624 |
< |
samples/water/spce/SPCEinit.in, samples/water/spce/spce.bass, |
625 |
< |
samples/water/spce/water.mdl, samples/water/ssde/256init.in, |
626 |
< |
samples/water/ssde/ssde.bass, samples/water/ssde/water.mdl, |
627 |
< |
samples/water/tip4p/TP4init.in, samples/water/tip4p/tp4.bass, |
628 |
< |
samples/water/tip4p/water.mdl, scripts/cleanSrc, scripts/cvs2cl.pl, |
629 |
< |
scripts/sfmakedepend, src/Make.dep, src/Makefile, src/Makefile.in, |
630 |
< |
src/oopse.cpp, src/oose.cpp, src/MPIobj/dummy, src/obj/dummy, |
631 |
< |
third-party/Makefile, third-party/Makefile.in, |
632 |
< |
third-party/mt19937ar.c, utils/Dump2XYZ.cpp, utils/Dump2XYZ.ggo, |
633 |
< |
utils/Dump2XYZCmd.c, utils/Dump2XYZCmd.h, utils/Make.dep, |
634 |
< |
utils/Makefile, utils/Makefile.in, utils/quickLate.c, utils/zsub, |
635 |
< |
utils/MPIobj/placeHolder, utils/obj/placeHolder, |
636 |
< |
utils/sysbuilder/Make.dep, utils/sysbuilder/Makefile, |
637 |
< |
utils/sysbuilder/Makefile.in, utils/sysbuilder/MoLocator.cpp, |
638 |
< |
utils/sysbuilder/MoLocator.hpp, utils/sysbuilder/cmdline.c, |
639 |
< |
utils/sysbuilder/cmdline.h, utils/sysbuilder/latticeBilayer.cpp, |
640 |
< |
utils/sysbuilder/latticeBuilder.cpp, |
641 |
< |
utils/sysbuilder/latticeBuilder.hpp, |
642 |
< |
utils/sysbuilder/nanoBuilder.cpp, utils/sysbuilder/nanoBuilder.hpp, |
643 |
< |
utils/sysbuilder/randomBilayer.cpp, utils/sysbuilder/sysBuild.cpp, |
644 |
< |
utils/sysbuilder/sysBuild.ggo, utils/sysbuilder/sysBuild.hpp, |
645 |
< |
utils/sysbuilder/MPIobj/placeHolder, |
646 |
< |
utils/sysbuilder/obj/placeHolder: Initial revision |
1118 |
> |
forceFields/Makefile.in, forceFields/Ni.u3.funcfl, |
1119 |
> |
forceFields/Ni.u6.funcfl, forceFields/Pd.VC.funcfl, |
1120 |
> |
forceFields/Pd.u6.funcfl, forceFields/Pt.u3.funcfl, |
1121 |
> |
forceFields/Pt.u6.funcfl, forceFields/WATER.frc, scripts/cleanSrc, |
1122 |
> |
scripts/cvs2cl.pl, scripts/makers, scripts/sfmakedepend, |
1123 |
> |
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
1124 |
> |
ac-tools/config.sub, ac-tools/configure.in, ac-tools/fortran90.m4, |
1125 |
> |
ac-tools/install-sh, ac-tools/shtool, doc/OOPSE.pdf, |
1126 |
> |
forceFields/Al.VC.funcfl, forceFields/Au.VC.funcfl, |
1127 |
> |
forceFields/Au.u3.funcfl, forceFields/LJFF.frc, |
1128 |
> |
forceFields/Ni.VC.funcfl, forceFields/Pd.u3.funcfl, |
1129 |
> |
forceFields/Pt.VC.funcfl: Initial revision |
1130 |
|
|