1 |
mmeineke |
568 |
2003-06-25 16:12 mmeineke |
2 |
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3 |
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* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
4 |
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to Harmonic bonds in the DUFF frc file |
5 |
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6 |
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fixed constraints. |
7 |
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8 |
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2003-06-25 16:11 mmeineke |
9 |
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10 |
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* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
11 |
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the DUFF frc file |
12 |
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13 |
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2003-06-24 17:51 gezelter |
14 |
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15 |
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* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
16 |
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17 |
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2003-06-24 14:57 mmeineke |
18 |
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19 |
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* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
20 |
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libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
21 |
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the DUFF forcefield and BondExtensions.cpp |
22 |
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23 |
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2003-06-23 16:24 mmeineke |
24 |
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25 |
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* libmdtools/Integrator.cpp: Doing some work to debug the |
26 |
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constraint code. |
27 |
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28 |
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2003-06-20 15:50 gezelter |
29 |
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30 |
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* libmdtools/Integrator.hpp: NPT fix |
31 |
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32 |
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2003-06-20 15:29 mmeineke |
33 |
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34 |
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* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
35 |
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libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
36 |
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libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
37 |
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libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
38 |
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libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
39 |
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integrator and NVT seem to be working now. |
40 |
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41 |
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2003-06-20 11:49 gezelter |
42 |
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43 |
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* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
44 |
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45 |
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2003-06-19 17:02 mmeineke |
46 |
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47 |
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* forceFields/DUFF.frc, forceFields/LJFF.frc, |
48 |
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forceFields/LJ_FF.frc, forceFields/Makefile, |
49 |
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forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
50 |
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libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
51 |
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libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
52 |
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libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, |
53 |
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libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
54 |
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forcefield names. |
55 |
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56 |
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2003-06-19 14:21 mmeineke |
57 |
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58 |
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* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
59 |
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finished the basics of the integrator and SimSetup.cpp |
60 |
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61 |
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2003-06-19 14:11 mmeineke |
62 |
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63 |
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* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
64 |
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up / get it to work with the new Integrator. |
65 |
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66 |
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2003-06-18 17:20 mmeineke |
67 |
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68 |
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* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
69 |
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output times. |
70 |
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71 |
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2003-06-17 16:56 mmeineke |
72 |
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73 |
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* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
74 |
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fro the ghost Bend in TraPPE_Ex |
75 |
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76 |
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some work on the integrator. ( incomplete) |
77 |
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78 |
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2003-06-17 16:55 mmeineke |
79 |
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80 |
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* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
81 |
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Bend in TraPPE_Ex |
82 |
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83 |
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2003-06-04 16:06 mmeineke |
84 |
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85 |
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* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
86 |
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constrainB to the Symplectic integrator |
87 |
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88 |
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2003-05-30 16:32 mmeineke |
89 |
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90 |
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* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
91 |
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the basic integrator. |
92 |
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93 |
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bilayerSys.cpp altered for building tb3. |
94 |
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95 |
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2003-05-30 16:31 mmeineke |
96 |
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97 |
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* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
98 |
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TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
99 |
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modifiying Symplectic to become the basic integrator. |
100 |
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101 |
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2003-05-30 15:19 mmeineke |
102 |
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103 |
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* libmdtools/Integrator.hpp: added some member variables for |
104 |
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position, velocity, etc. |
105 |
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106 |
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2003-05-30 14:07 mmeineke |
107 |
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108 |
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* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
109 |
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is now derived from Integrator |
110 |
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111 |
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2003-05-20 11:44 mmeineke |
112 |
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113 |
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* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
114 |
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115 |
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2003-05-17 11:57 mmeineke |
116 |
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117 |
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* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
118 |
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working |
119 |
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120 |
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2003-05-16 16:37 mmeineke |
121 |
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122 |
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* utils/bilayerSys.cpp: still working on the bilayer code |
123 |
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124 |
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2003-05-16 09:28 mmeineke |
125 |
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126 |
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* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
127 |
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work to overhaul sysbuild. |
128 |
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129 |
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2003-05-13 16:23 mmeineke |
130 |
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131 |
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* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
132 |
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133 |
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2003-05-13 15:47 mmeineke |
134 |
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135 |
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* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
136 |
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beadLipid/water.mdl: Added bead lipid model to the sample directory |
137 |
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138 |
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2003-05-13 15:34 mmeineke |
139 |
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140 |
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* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
141 |
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the Trappe extended force field |
142 |
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143 |
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2003-05-13 12:01 mmeineke |
144 |
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145 |
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* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
146 |
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TraPPe_Ex forceField |
147 |
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148 |
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2003-05-09 14:51 mmeineke |
149 |
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150 |
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* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
151 |
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there were some duplicate entries |
152 |
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153 |
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added a two chain lipid to the lipid.mdl in sample |
154 |
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155 |
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2003-05-09 14:51 mmeineke |
156 |
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157 |
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* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
158 |
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there were some duplicate entries |
159 |
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160 |
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2003-05-09 11:56 mmeineke |
161 |
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162 |
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* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
163 |
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configure script |
164 |
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165 |
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added the CH branching group to the TraPPE_Ex fource field |
166 |
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167 |
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2003-05-09 11:55 mmeineke |
168 |
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169 |
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* ac-tools/configure.in: added the utils subdirectory to the |
170 |
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configure script |
171 |
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172 |
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2003-04-25 11:02 mmeineke |
173 |
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174 |
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* utils/bilayerSys.cpp: i quick fix to th distance in the random |
175 |
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bilayer builder |
176 |
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177 |
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2003-04-24 21:00 mmeineke |
178 |
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179 |
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* libmdtools/f_verlet_constrained.F90: added a new test for |
180 |
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constraint failure |
181 |
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182 |
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2003-04-17 16:54 mmeineke |
183 |
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184 |
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* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
185 |
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utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
186 |
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utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
187 |
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build our systems |
188 |
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189 |
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2003-04-16 16:11 mmeineke |
190 |
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191 |
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* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
192 |
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193 |
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2003-04-15 16:47 mmeineke |
194 |
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195 |
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* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
196 |
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and sysBuild both will build now. woot! |
197 |
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198 |
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2003-04-15 16:20 mmeineke |
199 |
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200 |
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* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
201 |
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bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
202 |
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203 |
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sysBuild still need to write the bass file. |
204 |
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205 |
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MoLocator.cpp is currently empty |
206 |
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207 |
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2003-04-15 15:40 chuckv |
208 |
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209 |
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* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
210 |
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forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
211 |
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forceFields/pdu3.eam, forceFields/ptu3.eam, |
212 |
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libmdtools/ForceFields.hpp: Added eam force files... |
213 |
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214 |
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2003-04-15 11:37 chuckv |
215 |
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216 |
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* libmdtools/EAM_FF.cpp: More eam work. |
217 |
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218 |
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2003-04-14 16:22 mmeineke |
219 |
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220 |
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* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
221 |
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utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
222 |
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working on the system builder |
223 |
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224 |
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2003-04-14 16:16 chuckv |
225 |
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226 |
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* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
227 |
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ordering on NVT calculation in integrators. |
228 |
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229 |
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2003-04-14 14:51 mmeineke |
230 |
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231 |
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* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
232 |
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obj/placeHolder: working on a system builder |
233 |
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234 |
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2003-04-14 14:04 mmeineke |
235 |
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236 |
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* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
237 |
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238 |
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added sysBuild to the utils Makefile |
239 |
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240 |
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2003-04-14 14:03 mmeineke |
241 |
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242 |
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* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
243 |
|
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Ghost bends to the TraPPE_Ex forceField |
244 |
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245 |
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2003-04-14 13:19 chuckv |
246 |
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247 |
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* libmdtools/calc_eam.F90: Added first mangling of EAM. |
248 |
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249 |
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2003-04-11 13:46 mmeineke |
250 |
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251 |
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* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
252 |
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simulation_module.F90: fixed a memory bug in Fortran, where |
253 |
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molMembershipArray was declared nLocal instead of nGlobal. |
254 |
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255 |
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2003-04-11 10:16 gezelter |
256 |
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257 |
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* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
258 |
|
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SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
259 |
|
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fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
260 |
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for NPT |
261 |
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262 |
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2003-04-10 15:08 mmeineke |
263 |
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264 |
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* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
265 |
|
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globalIndex counter to Molecule |
266 |
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267 |
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2003-04-10 11:35 gezelter |
268 |
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269 |
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* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
270 |
|
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ConstantStress |
271 |
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272 |
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2003-04-10 11:27 mmeineke |
273 |
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274 |
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* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
275 |
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caused a miscalculation of nLocal. |
276 |
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277 |
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2003-04-10 11:21 mmeineke |
278 |
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279 |
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* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
280 |
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do_Forces.F90: fixed a bug in symplectic, where presure was only |
281 |
|
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being calculated the first time through. |
282 |
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283 |
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2003-04-09 11:20 chuckv |
284 |
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285 |
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* samples/alkane/alkanes.mdl: added pentane to the alkane model |
286 |
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file |
287 |
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288 |
|
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2003-04-09 08:59 gezelter |
289 |
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290 |
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* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
291 |
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Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
292 |
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293 |
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2003-04-08 23:06 gezelter |
294 |
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295 |
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* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
296 |
|
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ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
297 |
|
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SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, |
298 |
|
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Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
299 |
|
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calc_reaction_field.F90, calc_sticky_pair.F90, |
300 |
|
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fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
301 |
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NVT |
302 |
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303 |
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2003-04-08 17:38 chuckv |
304 |
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|
305 |
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* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
306 |
|
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libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
307 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
308 |
|
|
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
309 |
|
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(kinda)... |
310 |
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311 |
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2003-04-08 16:35 gezelter |
312 |
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313 |
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* libBASS/Globals.cpp, libBASS/Globals.hpp, |
314 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
315 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
316 |
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|
317 |
|
|
2003-04-08 12:16 chuckv |
318 |
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|
319 |
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* libmdtools/: do_Forces.F90, neighborLists.F90, |
320 |
|
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simulation_module.F90: Moved expand neighborlist to init_FF. |
321 |
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322 |
|
|
2003-04-08 10:20 chuckv |
323 |
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|
324 |
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* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
325 |
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NVT |
326 |
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327 |
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2003-04-08 09:39 gezelter |
328 |
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329 |
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* libmdtools/Verlet.cpp: fixes for nvt / npt |
330 |
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331 |
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2003-04-08 09:34 gezelter |
332 |
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|
333 |
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* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
334 |
|
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Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
335 |
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336 |
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2003-04-08 07:50 gezelter |
337 |
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338 |
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* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
339 |
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340 |
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2003-04-08 07:44 gezelter |
341 |
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|
342 |
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* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
343 |
|
|
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
344 |
|
|
NVT and NPT ensembles |
345 |
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346 |
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2003-04-07 16:42 gezelter |
347 |
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|
348 |
|
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* libBASS/Globals.cpp, libBASS/Globals.hpp, |
349 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
350 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
351 |
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352 |
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2003-04-07 16:20 mmeineke |
353 |
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354 |
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* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
355 |
|
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portion of SSD. |
356 |
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357 |
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2003-04-07 16:16 mmeineke |
358 |
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|
359 |
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* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
360 |
|
|
doing some testing in sticky through Symplectic. |
361 |
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362 |
|
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2003-04-07 15:51 gezelter |
363 |
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|
364 |
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* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
365 |
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|
366 |
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|
2003-04-07 15:50 chuckv |
367 |
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368 |
|
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* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
369 |
|
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tau and virial. |
370 |
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371 |
|
|
2003-04-07 15:06 mmeineke |
372 |
|
|
|
373 |
|
|
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
374 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
375 |
|
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
376 |
|
|
src/Makefile: bug fixes |
377 |
|
|
|
378 |
|
|
2003-04-07 11:56 gezelter |
379 |
|
|
|
380 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
381 |
|
|
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
382 |
|
|
Many fixes to add extended system |
383 |
|
|
|
384 |
|
|
2003-04-07 09:30 gezelter |
385 |
|
|
|
386 |
|
|
* src/Makefile: Fixed a bug caused by my experimentation |
387 |
|
|
|
388 |
|
|
2003-04-07 09:30 gezelter |
389 |
|
|
|
390 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
391 |
|
|
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
392 |
|
|
Added ExtendedSystem infrastructure for NPT and NVT calculations |
393 |
|
|
|
394 |
|
|
2003-04-07 09:30 gezelter |
395 |
|
|
|
396 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
397 |
|
|
|
398 |
|
|
2003-04-04 23:07 gezelter |
399 |
|
|
|
400 |
|
|
* src/Makefile: final mods to try a fortran compiler |
401 |
|
|
|
402 |
|
|
2003-04-04 22:39 gezelter |
403 |
|
|
|
404 |
|
|
* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, |
405 |
|
|
fortranWrapDefines.hpp: Bug fixes for simulation module rewrites |
406 |
|
|
|
407 |
|
|
2003-04-04 21:56 gezelter |
408 |
|
|
|
409 |
|
|
* libmdtools/: Makefile, atype_module.F90, do_Forces.F90, |
410 |
|
|
fortranWrappers.cpp, wrappers.F90: bug fixes for compilation |
411 |
|
|
|
412 |
|
|
2003-04-04 21:45 gezelter |
413 |
|
|
|
414 |
|
|
* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug |
415 |
|
|
fixes to fortran wrappers |
416 |
|
|
|
417 |
|
|
2003-04-04 17:22 chuckv |
418 |
|
|
|
419 |
|
|
* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
420 |
|
|
calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, |
421 |
|
|
do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, |
422 |
|
|
simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets |
423 |
|
|
smarter, fortran gets dumber... |
424 |
|
|
|
425 |
|
|
2003-04-04 14:57 mmeineke |
426 |
|
|
|
427 |
|
|
* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, |
428 |
|
|
neighborLists.F90: fixed a memory read bug in neighborlist |
429 |
|
|
|
430 |
|
|
2003-04-04 14:47 gezelter |
431 |
|
|
|
432 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
433 |
|
|
SimInfo.hpp, Thermo.cpp: Changes for Extended System |
434 |
|
|
|
435 |
|
|
2003-04-04 14:16 gezelter |
436 |
|
|
|
437 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
438 |
|
|
SimInfo.hpp: Fixes for ExtendedSystem |
439 |
|
|
|
440 |
|
|
2003-04-03 20:57 gezelter |
441 |
|
|
|
442 |
|
|
* libmdtools/ExtendedSystem.hpp: Added extended system header |
443 |
|
|
|
444 |
|
|
2003-04-03 20:57 gezelter |
445 |
|
|
|
446 |
|
|
* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes |
447 |
|
|
for extended system code |
448 |
|
|
|
449 |
|
|
2003-04-03 18:49 gezelter |
450 |
|
|
|
451 |
|
|
* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to |
452 |
|
|
extendedsystem |
453 |
|
|
|
454 |
|
|
2003-04-03 17:19 mmeineke |
455 |
|
|
|
456 |
|
|
* libmdtools/Molecule.hpp: added some little fixes here and there. |
457 |
|
|
|
458 |
|
|
2003-04-03 17:01 mmeineke |
459 |
|
|
|
460 |
|
|
* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before |
461 |
|
|
initialize bug. |
462 |
|
|
|
463 |
|
|
2003-04-03 16:12 mmeineke |
464 |
|
|
|
465 |
|
|
* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just |
466 |
|
|
little things like deleteing unused variables and such. |
467 |
|
|
|
468 |
|
|
2003-04-03 15:57 mmeineke |
469 |
|
|
|
470 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to |
471 |
|
|
simError.h also some fixes to Molecule.hpp |
472 |
|
|
|
473 |
|
|
2003-04-03 15:57 mmeineke |
474 |
|
|
|
475 |
|
|
* libBASS/simError.h: a few fixes to simError.h |
476 |
|
|
|
477 |
|
|
2003-04-03 15:21 mmeineke |
478 |
|
|
|
479 |
|
|
* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, |
480 |
|
|
libBASS/simError.h, libmdtools/DumpWriter.cpp, |
481 |
|
|
libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, |
482 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, |
483 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, |
484 |
|
|
src/Makefile, src/oopse.cpp: fixed some small things with |
485 |
|
|
simError.h |
486 |
|
|
|
487 |
|
|
2003-04-03 15:19 gezelter |
488 |
|
|
|
489 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT |
490 |
|
|
|
491 |
|
|
2003-04-03 14:58 gezelter |
492 |
|
|
|
493 |
|
|
* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for |
494 |
|
|
now) |
495 |
|
|
|
496 |
|
|
2003-04-03 08:42 gezelter |
497 |
|
|
|
498 |
|
|
* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: |
499 |
|
|
Changed Readme, added some files |
500 |
|
|
|
501 |
|
|
2003-04-02 17:19 mmeineke |
502 |
|
|
|
503 |
|
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, |
504 |
|
|
Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: |
505 |
|
|
dipoles mostly work, but there is a memory leak somewhere. |
506 |
|
|
|
507 |
|
|
2003-04-02 10:01 mmeineke |
508 |
|
|
|
509 |
|
|
* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting |
510 |
|
|
the proper atomIdents. |
511 |
|
|
|
512 |
|
|
2003-04-01 11:50 chuckv |
513 |
|
|
|
514 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
515 |
|
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
516 |
|
|
samples/argon/argon.bass: more bug fixes.... |
517 |
|
|
|
518 |
|
|
2003-04-01 11:49 mmeineke |
519 |
|
|
|
520 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed |
521 |
|
|
DumpWriter to be more robust to errors. also added a little |
522 |
|
|
namespace to InitFromFile to wrap it's helper functions in MPI |
523 |
|
|
|
524 |
|
|
2003-03-31 17:09 chuckv |
525 |
|
|
|
526 |
|
|
* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local |
527 |
|
|
not zeroed. |
528 |
|
|
|
529 |
|
|
2003-03-31 16:50 chuckv |
530 |
|
|
|
531 |
|
|
* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, |
532 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
533 |
|
|
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
534 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
535 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, |
536 |
|
|
samples/alkane/butane.bass: Fixes in MPI force calc and in |
537 |
|
|
Trappe_Ex parsing. |
538 |
|
|
|
539 |
|
|
2003-03-28 17:34 chuckv |
540 |
|
|
|
541 |
|
|
* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp |
542 |
|
|
|
543 |
|
|
2003-03-28 16:45 chuckv |
544 |
|
|
|
545 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
546 |
|
|
libmdtools/InitializeFromFile.cpp: Bug fixes in read-write |
547 |
|
|
routines. |
548 |
|
|
|
549 |
|
|
2003-03-28 14:33 mmeineke |
550 |
|
|
|
551 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, |
552 |
|
|
Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a |
553 |
|
|
bug where the Excludes were not being created properly |
554 |
|
|
|
555 |
|
|
2003-03-28 14:30 chuckv |
556 |
|
|
|
557 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
558 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, |
559 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes |
560 |
|
|
and debugging mpi read write from file. |
561 |
|
|
|
562 |
|
|
2003-03-28 10:28 mmeineke |
563 |
|
|
|
564 |
|
|
* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range |
565 |
|
|
interactions in Trappe |
566 |
|
|
|
567 |
|
|
2003-03-27 18:33 chuckv |
568 |
|
|
|
569 |
|
|
* libmdtools/: SimSetup.cpp, mpiSimulation.cpp, |
570 |
|
|
mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. |
571 |
|
|
|
572 |
|
|
2003-03-27 17:16 mmeineke |
573 |
|
|
|
574 |
|
|
* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where |
575 |
|
|
excludes were not being initialized |
576 |
|
|
|
577 |
|
|
2003-03-27 16:52 mmeineke |
578 |
|
|
|
579 |
|
|
* src/Makefile: [no log message] |
580 |
|
|
|
581 |
|
|
2003-03-27 16:52 mmeineke |
582 |
|
|
|
583 |
|
|
* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. |
584 |
|
|
|
585 |
|
|
2003-03-27 16:07 mmeineke |
586 |
|
|
|
587 |
|
|
* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, |
588 |
|
|
Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, |
589 |
|
|
Verlet.cpp: fixed the compile time bugs, Source builds and links |
590 |
|
|
|
591 |
|
|
2003-03-27 15:48 mmeineke |
592 |
|
|
|
593 |
|
|
* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few |
594 |
|
|
more bugs. |
595 |
|
|
|
596 |
|
|
2003-03-27 15:40 mmeineke |
597 |
|
|
|
598 |
|
|
* libmdtools/Molecule.cpp: added the Molecule.cpp file |
599 |
|
|
|
600 |
|
|
2003-03-27 15:39 mmeineke |
601 |
|
|
|
602 |
|
|
* libmdtools/: Makefile, Molecule.hpp: fixed the makefile |
603 |
|
|
|
604 |
|
|
2003-03-27 15:36 mmeineke |
605 |
|
|
|
606 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
607 |
|
|
ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, |
608 |
|
|
SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs |
609 |
|
|
|
610 |
|
|
2003-03-27 15:12 mmeineke |
611 |
|
|
|
612 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
613 |
|
|
Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, |
614 |
|
|
Verlet.cpp: I have implemeted Molecules everywhere I could remember |
615 |
|
|
to. will now attempt to compile. |
616 |
|
|
|
617 |
|
|
2003-03-27 14:21 mmeineke |
618 |
|
|
|
619 |
|
|
* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, |
620 |
|
|
SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished |
621 |
|
|
updating SimSetup to initialize and use the new MPI division of |
622 |
|
|
labour, and Molecule class |
623 |
|
|
|
624 |
|
|
2003-03-27 12:55 mmeineke |
625 |
|
|
|
626 |
|
|
* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to |
627 |
|
|
use Molecule |
628 |
|
|
|
629 |
|
|
2003-03-27 12:32 mmeineke |
630 |
|
|
|
631 |
|
|
* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, |
632 |
|
|
SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been |
633 |
|
|
converted to the new Molecule model. TraPPE_Ex is currently being |
634 |
|
|
updated. SimSetups routines are writtten, but not yet called. |
635 |
|
|
|
636 |
|
|
2003-03-27 10:07 gezelter |
637 |
|
|
|
638 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
639 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom |
640 |
|
|
numbering in MPI |
641 |
|
|
|
642 |
|
|
2003-03-27 09:30 mmeineke |
643 |
|
|
|
644 |
|
|
* libmdtools/mpiSimulation.cpp: little bug fixes here and there. |
645 |
|
|
|
646 |
|
|
2003-03-26 20:49 gezelter |
647 |
|
|
|
648 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to |
649 |
|
|
fileio for MPI |
650 |
|
|
|
651 |
|
|
2003-03-26 18:14 gezelter |
652 |
|
|
|
653 |
|
|
* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, |
654 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug |
655 |
|
|
fixes many bug fixes |
656 |
|
|
|
657 |
|
|
2003-03-26 17:24 gezelter |
658 |
|
|
|
659 |
|
|
* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on |
660 |
|
|
sequence of atoms on the other processors. Node 0 now fires |
661 |
|
|
potatoes at other processors to get them to send french fries back. |
662 |
|
|
|
663 |
|
|
2003-03-26 17:02 mmeineke |
664 |
|
|
|
665 |
|
|
* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for |
666 |
|
|
making the molecules is in place. ForceField needs to be updated |
667 |
|
|
next. |
668 |
|
|
|
669 |
|
|
2003-03-26 16:54 mmeineke |
670 |
|
|
|
671 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of |
672 |
|
|
the "static" bugs in Atom and Exclude |
673 |
|
|
|
674 |
|
|
2003-03-26 16:50 mmeineke |
675 |
|
|
|
676 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, |
677 |
|
|
SimSetup.cpp: still working on the SimSetup routine. also fixed |
678 |
|
|
some things in Exclude.hpp |
679 |
|
|
|
680 |
|
|
2003-03-26 16:24 gezelter |
681 |
|
|
|
682 |
|
|
* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp |
683 |
|
|
|
684 |
|
|
2003-03-26 16:23 gezelter |
685 |
|
|
|
686 |
|
|
* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom |
687 |
|
|
and Exclude list |
688 |
|
|
|
689 |
|
|
2003-03-26 16:04 gezelter |
690 |
|
|
|
691 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and |
692 |
|
|
delete ranges of atoms |
693 |
|
|
|
694 |
|
|
2003-03-26 15:45 mmeineke |
695 |
|
|
|
696 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class |
697 |
|
|
with static arrays similar to the Atom class |
698 |
|
|
|
699 |
|
|
2003-03-26 15:22 mmeineke |
700 |
|
|
|
701 |
|
|
* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm |
702 |
|
|
overhauling the molecule class to contain it's own bonds, bends, |
703 |
|
|
and torsions. |
704 |
|
|
|
705 |
|
|
may god have mercy on my soul. |
706 |
|
|
|
707 |
|
|
2003-03-26 14:34 chuckv |
708 |
|
|
|
709 |
|
|
* libmdtools/mpiSimulation.cpp: Finished globalIndex. |
710 |
|
|
|
711 |
|
|
2003-03-26 13:02 gezelter |
712 |
|
|
|
713 |
|
|
* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, |
714 |
|
|
mpiSimulation.hpp: MPI stuff for passing out molecules |
715 |
|
|
|
716 |
|
|
2003-03-26 11:12 chuckv |
717 |
|
|
|
718 |
|
|
* libmdtools/mpiSimulation.cpp: working on load balancing |
719 |
|
|
|
720 |
|
|
2003-03-26 10:37 chuckv |
721 |
|
|
|
722 |
|
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
723 |
|
|
samples/argon/argon.bass: Fixes for Parallel thermalization |
724 |
|
|
|
725 |
|
|
2003-03-26 09:55 mmeineke |
726 |
|
|
|
727 |
|
|
* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in |
728 |
|
|
THermo.cpp |
729 |
|
|
|
730 |
|
|
2003-03-25 17:54 chuckv |
731 |
|
|
|
732 |
|
|
* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation |
733 |
|
|
of potential energy and temperature. |
734 |
|
|
|
735 |
|
|
2003-03-25 09:29 mmeineke |
736 |
|
|
|
737 |
|
|
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
738 |
|
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
739 |
|
|
|
740 |
|
|
2003-03-25 09:29 mmeineke |
741 |
|
|
|
742 |
|
|
* libBASS/MPIobj/dummy: added dummy files to keep the build |
743 |
|
|
deirectories from being pruned. |
744 |
|
|
|
745 |
|
|
2003-03-24 20:07 gezelter |
746 |
|
|
|
747 |
|
|
* samples/Makefile: moving tests to samples |
748 |
|
|
|
749 |
|
|
2003-03-24 20:06 gezelter |
750 |
|
|
|
751 |
|
|
* samples/: alkane/Makefile, alkane/alkanes.mdl, |
752 |
|
|
alkane/butane.bass, alkane/init_butane.eor, argon/Makefile, |
753 |
|
|
argon/argon.bass, argon/init_argon.eor, argon/lj.mdl, |
754 |
|
|
lipid/5x5.bass, lipid/Makefile, lipid/init_5x5.eor, |
755 |
|
|
lipid/lipid.mdl, lipid/water.mdl, water/Makefile, |
756 |
|
|
water/init_ssd.eor, water/ssd.bass, water/water.mdl: moved tests to |
757 |
|
|
samples |
758 |
|
|
|
759 |
|
|
2003-03-24 19:51 gezelter |
760 |
|
|
|
761 |
|
|
* ac-tools/configure.in: Tests are becoming samples |
762 |
|
|
|
763 |
|
|
2003-03-24 19:46 gezelter |
764 |
|
|
|
765 |
|
|
* ac-tools/Make.conf.in: Added makefiles in tests directories |
766 |
|
|
|
767 |
|
|
2003-03-24 16:55 gezelter |
768 |
|
|
|
769 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, |
770 |
|
|
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, |
771 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, |
772 |
|
|
libmdtools/calc_reaction_field.F90, |
773 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
774 |
|
|
libmdtools/simulation_module.F90: electrostatic changes for dipole |
775 |
|
|
/ RF separation |
776 |
|
|
|
777 |
|
|
2003-03-24 13:33 mmeineke |
778 |
|
|
|
779 |
|
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
780 |
|
|
do_Forces.F90: little bug fixes here and there |
781 |
|
|
|
782 |
|
|
2003-03-24 10:26 mmeineke |
783 |
|
|
|
784 |
|
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
785 |
|
|
where short range interactions were not being calculated. |
786 |
|
|
|
787 |
|
|
removed some debug print statements |
788 |
|
|
|
789 |
|
|
2003-03-21 17:11 chuckv |
790 |
|
|
|
791 |
|
|
* libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, |
792 |
|
|
do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: |
793 |
|
|
various write statements for debugging |
794 |
|
|
|
795 |
|
|
2003-03-21 16:26 chuckv |
796 |
|
|
|
797 |
|
|
* forceFields/Makefile: added links to the makefile in forceFields |
798 |
|
|
|
799 |
|
|
2003-03-21 15:52 gezelter |
800 |
|
|
|
801 |
|
|
* ac-tools/Make.conf.in, ac-tools/configure.in, |
802 |
|
|
libmdtools/Makefile: Fixed F_MACH_DEP bug |
803 |
|
|
|
804 |
|
|
2003-03-21 15:37 gezelter |
805 |
|
|
|
806 |
|
|
* ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, |
807 |
|
|
ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, |
808 |
|
|
libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, |
809 |
|
|
src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, |
810 |
|
|
autoconf fixes |
811 |
|
|
|
812 |
gezelter |
385 |
2003-03-21 14:58 gezelter |
813 |
mmeineke |
377 |
|
814 |
gezelter |
385 |
* LICENSE: Added license file |
815 |
|
|
|
816 |
|
|
2003-03-21 14:55 gezelter |
817 |
|
|
|
818 |
|
|
* forceFields/Makefile: Fixed makefile |
819 |
|
|
|
820 |
|
|
2003-03-21 14:49 gezelter |
821 |
|
|
|
822 |
|
|
* forceFields/Makefile: Makefile for forceFields |
823 |
|
|
|
824 |
|
|
2003-03-21 14:42 gezelter |
825 |
|
|
|
826 |
|
|
* README: Readme changes |
827 |
|
|
|
828 |
|
|
2003-03-21 12:52 mmeineke |
829 |
|
|
|
830 |
|
|
* src/Makefile: [no log message] |
831 |
|
|
|
832 |
|
|
2003-03-21 12:52 mmeineke |
833 |
|
|
|
834 |
|
|
* libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends |
835 |
|
|
|
836 |
|
|
2003-03-21 12:42 mmeineke |
837 |
|
|
|
838 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
839 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
840 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
841 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
842 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
843 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
844 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
845 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
846 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
847 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
848 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
849 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
850 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
851 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
852 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
853 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
854 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
855 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
856 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
857 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
858 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
859 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
860 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
861 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
862 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
863 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
864 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
865 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
866 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
867 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
868 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
869 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
870 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
871 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
872 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
873 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
874 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
875 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
876 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
877 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
878 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
879 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
880 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
881 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
882 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
883 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
884 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
885 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
886 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
887 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
888 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
889 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
890 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
891 |
|
|
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
892 |
|
|
Tree |
893 |
|
|
|
894 |
|
|
2003-03-21 12:42 mmeineke |
895 |
|
|
|
896 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
897 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
898 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
899 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
900 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
901 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
902 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
903 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
904 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
905 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
906 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
907 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
908 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
909 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
910 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
911 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
912 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
913 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
914 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
915 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
916 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
917 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
918 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
919 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
920 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
921 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
922 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
923 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
924 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
925 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
926 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
927 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
928 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
929 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
930 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
931 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
932 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
933 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
934 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
935 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
936 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
937 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
938 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
939 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
940 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
941 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
942 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
943 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
944 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
945 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
946 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
947 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
948 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
949 |
|
|
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
950 |
|
|
revision |
951 |
|
|
|