1 |
tim |
837 |
2003-10-24 18:17 mmeineke |
2 |
gezelter |
760 |
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3 |
tim |
837 |
* utils/sysbuilder/: Make.dep, Makefile.in, MoLocator.cpp, |
4 |
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MoLocator.hpp, QuickBass.cpp, QuickBass.hpp, bilayerSys.cpp, |
5 |
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latticeBilayer.cpp, latticeBuilder.cpp, sysBuild.cpp: put |
6 |
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QuickBass, MoLocator, and latticeBuilder into a Builder Library |
7 |
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overhauled latticeBilayer into its own program. Removed sysBuild |
8 |
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from the Makefile |
9 |
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10 |
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2003-10-24 13:36 gezelter |
11 |
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12 |
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* utils/sysbuilder/: bilayerSys.cpp, latticeBuilder.cpp, |
13 |
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latticeBuilder.hpp, sysBuild.cpp, sysBuild.hpp: work on bilayer |
14 |
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builder |
15 |
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16 |
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2003-10-24 13:35 gezelter |
17 |
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18 |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in: fixed a |
19 |
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merge problem |
20 |
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21 |
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2003-10-23 15:57 mmeineke |
22 |
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23 |
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* samples/metals/Makefile.in: added eam ForceField files to the |
24 |
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init |
25 |
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26 |
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fixed an eam mpi parmeter setup bug |
27 |
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28 |
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added the init file to the makefile |
29 |
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30 |
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2003-10-23 15:57 mmeineke |
31 |
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* libmdtools/: EAM_FF.cpp, SimSetup.cpp: added eam ForceField files |
33 |
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to the init |
34 |
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35 |
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fixed an eam mpi parmeter setup bug |
36 |
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37 |
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2003-10-23 15:57 mmeineke |
38 |
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39 |
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* forceFields/Makefile.in: added eam ForceField files to the init |
40 |
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41 |
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2003-10-22 17:17 mmeineke |
42 |
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43 |
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* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Makefile.in, |
44 |
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NPTxym.cpp, NPTxyz.cpp, NPTzm.cpp, SimSetup.cpp: added a new NPT |
45 |
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integrator, NPTxyz. It scales the x, y, and z direction sepeartely. |
46 |
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no box skew allowed. |
47 |
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48 |
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2003-10-21 15:33 mmeineke |
49 |
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50 |
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* libBASS/Globals.cpp, libBASS/Globals.hpp, |
51 |
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libmdtools/SimSetup.cpp, staticProps/GofRtheta.cpp, |
52 |
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staticProps/PairCorrType.hpp: added useInitTime to the BASS syntax. |
53 |
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* useInitTime = false: sets the origin time to 0.0 regardless |
54 |
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of the time stamp in the .init file * default=> useInitTime = |
55 |
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true; |
56 |
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57 |
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2003-10-17 17:19 mmeineke |
58 |
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59 |
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* staticProps/: AllCorr.cpp, AllCorr.hpp, CorrWrap.cpp, GofR.cpp, |
60 |
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Makefile.in, PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
61 |
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staticProps.cpp, obj/placeholder: added the staticProps directory |
62 |
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to the build list for both configure and configure.in |
63 |
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64 |
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fixed a number of bugs in the staticProps code. gofr is now |
65 |
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working. |
66 |
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67 |
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2003-10-17 17:18 mmeineke |
68 |
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69 |
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* ac-tools/configure.in: added the staticProps directory to the |
70 |
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build list for both configure and configure.in |
71 |
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72 |
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2003-10-17 17:17 mmeineke |
73 |
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74 |
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* configure: added the staticProps directory to the build list |
75 |
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76 |
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2003-10-16 15:16 mmeineke |
77 |
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78 |
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* libmdtools/: DumpReader.cpp, DumpWriter.cpp, Exclude.cpp, |
79 |
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Integrator.cpp, Makefile.in, ReadWrite.hpp: Changed DumpReader to |
80 |
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use linked lists instead of a vector. |
81 |
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82 |
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Fixed the makefile to build DumpReader.cpp |
83 |
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84 |
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Removed a comment output in Exclude.cpp |
85 |
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86 |
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Modified DumpWriter and Integrator to write an eor file every time |
87 |
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a frame is written. This lets the .eor file represent the last |
88 |
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written frame of a simulation. |
89 |
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90 |
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2003-10-10 13:10 mmeineke |
91 |
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92 |
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* props/AllCorr.cpp, props/AllCorr.hpp, props/CorrWrap.cpp, |
93 |
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props/CorrWrap.hpp, props/GofR.cpp, props/PairCorrList.cpp, |
94 |
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props/PairCorrList.hpp, props/PairCorrType.cpp, |
95 |
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props/PairCorrType.hpp, props/staticProps.cpp, |
96 |
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staticProps/AllCorr.cpp, staticProps/AllCorr.hpp, |
97 |
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staticProps/CorrWrap.cpp, staticProps/CorrWrap.hpp, |
98 |
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staticProps/GofR.cpp, staticProps/Makefile.in, |
99 |
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staticProps/PairCorrList.cpp, staticProps/PairCorrList.hpp, |
100 |
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staticProps/PairCorrType.cpp, staticProps/PairCorrType.hpp, |
101 |
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staticProps/staticProps.cpp: removed the props directory, and moved |
102 |
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everything over to staticProps |
103 |
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104 |
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2003-10-09 18:09 mmeineke |
105 |
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106 |
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* libmdtools/Atom.hpp, props/AllCorr.cpp, props/AllCorr.hpp, |
107 |
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props/CorrWrap.cpp, props/CorrWrap.hpp, props/GofR.cpp, |
108 |
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props/PairCorrType.cpp, props/PairCorrType.hpp, |
109 |
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props/staticProps.cpp: Contiuned work on staticProps. should be in |
110 |
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a position where it will compile and run first runs. |
111 |
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112 |
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2003-10-04 14:46 chuckv |
113 |
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114 |
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* libmdtools/calc_eam.F90, libmdtools/do_Forces.F90, |
115 |
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samples/metals/Au.bass: Fixed bug in calc_eam. |
116 |
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117 |
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2003-10-04 14:08 chuckv |
118 |
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119 |
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* samples/metals/init_au.in: added Au init file for eam. |
120 |
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121 |
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2003-10-03 18:11 mmeineke |
122 |
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123 |
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* libmdtools/: StatWriter.cpp, Thermo.cpp, Thermo.hpp: removed |
124 |
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entahlpy from the statwriter and thermo. |
125 |
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126 |
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2003-10-03 18:02 mmeineke |
127 |
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128 |
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* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
129 |
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PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
130 |
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staticProps.cpp: changed the formating ogf the error statements in |
131 |
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simError |
132 |
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133 |
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added a function to get the maxCutoff |
134 |
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135 |
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near completion of the staticProps code. still needs the pair loop, |
136 |
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and the loop to allocate and read each frame. |
137 |
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138 |
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2003-10-03 18:02 mmeineke |
139 |
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140 |
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* libmdtools/SimInfo.hpp: changed the formating ogf the error |
141 |
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statements in simError |
142 |
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143 |
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added a function to get the maxCutoff |
144 |
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145 |
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2003-10-03 18:01 mmeineke |
146 |
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147 |
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* libBASS/simError.c: changed the formating ogf the error |
148 |
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statements in simError |
149 |
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150 |
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2003-10-02 18:06 mmeineke |
151 |
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152 |
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* props/: AllCorr.cpp, AllCorr.hpp, PairCorrList.cpp, |
153 |
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PairCorrList.hpp, PairCorrType.cpp, PairCorrType.hpp, |
154 |
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staticProps.cpp: finishing up the constructs needed to get this |
155 |
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program up and running |
156 |
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157 |
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2003-09-30 12:00 mmeineke |
158 |
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159 |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in: changed |
160 |
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f90Flags so they are no longer overwritten by the compiler. |
161 |
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162 |
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2003-09-29 18:06 mmeineke |
163 |
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164 |
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* libmdtools/fortranWrappers.cpp: added mpif90 mod check back same |
165 |
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for conifig.in |
166 |
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167 |
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fixed wrappers to extern "C" |
168 |
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169 |
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2003-09-29 18:06 mmeineke |
170 |
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171 |
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* ac-tools/configure.in: added mpif90 mod check back same for |
172 |
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conifig.in |
173 |
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174 |
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2003-09-29 18:05 mmeineke |
175 |
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176 |
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* configure: added mpif90 mod check back |
177 |
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178 |
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2003-09-29 17:16 mmeineke |
179 |
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180 |
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* configure, ac-tools/aclocal.m4, ac-tools/configure.in, |
181 |
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libBASS/BendStamp.cpp, libBASS/BondStamp.cpp, |
182 |
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libBASS/LinkedAssign.cpp, libBASS/LinkedCommand.cpp, |
183 |
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libBASS/MakeStamps.cpp, libBASS/TorsionStamp.cpp, |
184 |
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libBASS/ZconStamp.cpp, libBASS/simError.c, |
185 |
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libmdtools/Integrator.hpp, libmdtools/SimInfo.cpp, |
186 |
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libmdtools/SimInfo.hpp, libmdtools/calc_LJ_FF.F90, |
187 |
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libmdtools/fortranWrappers.cpp: fixed a lot of warnings and errors |
188 |
|
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found with SUN's SUNWspro.s1s7 |
189 |
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190 |
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2003-09-29 13:38 mmeineke |
191 |
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192 |
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* libmdtools/GenericData.hpp: light change in syntax. no |
193 |
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signifigant change. |
194 |
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195 |
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2003-09-25 17:17 mmeineke |
196 |
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197 |
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* libmdtools/: DirectionalAtom.cpp, Integrator.hpp: fixed some |
198 |
|
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additional remarks from icc -w3 (extra verbose output) |
199 |
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200 |
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2003-09-25 15:27 mmeineke |
201 |
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202 |
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* libBASS/parse_tree.c, libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
203 |
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libmdtools/DirectionalAtom.cpp, libmdtools/DumpWriter.cpp, |
204 |
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libmdtools/EAM_FF.cpp, libmdtools/ForceFields.cpp, |
205 |
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libmdtools/GenericData.cpp, libmdtools/InitializeFromFile.cpp, |
206 |
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libmdtools/Integrator.cpp, libmdtools/LJFF.cpp, |
207 |
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libmdtools/NPTf.cpp, libmdtools/NPTi.cpp, libmdtools/NPTzm.cpp, |
208 |
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libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
209 |
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libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
210 |
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libmdtools/ZConsWriter.cpp, libmdtools/ZConstraint.cpp, |
211 |
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libmdtools/mpiSimulation.cpp, src/oopse.cpp: cleaned things with |
212 |
|
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gcc -Wall and g++ -Wall |
213 |
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214 |
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2003-09-25 14:54 gezelter |
215 |
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216 |
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* configure, ac-tools/configure.in: fixed a bug in configure |
217 |
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218 |
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2003-09-25 12:42 gezelter |
219 |
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220 |
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* Makefile.in, configure, ac-tools/aclocal.m4, |
221 |
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ac-tools/configure.in, libBASS/Makefile.in, libmdtools/Makefile.in, |
222 |
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src/Makefile.in, utils/Makefile.in, utils/sysbuilder/Makefile.in: |
223 |
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fixes for configure |
224 |
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225 |
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2003-09-24 15:34 mmeineke |
226 |
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227 |
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* libmdtools/Integrator.cpp: moved readyCheck in the integrator so |
228 |
|
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that it is called before the first Statistics are written. |
229 |
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230 |
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2003-09-23 16:36 gezelter |
231 |
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232 |
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* src/Make.dep, utils/Make.dep, utils/sysbuilder/Make.dep: Added a |
233 |
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bunch of Make.dep files to CVS |
234 |
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235 |
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2003-09-23 16:34 mmeineke |
236 |
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237 |
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* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, |
238 |
|
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SimSetup.cpp: Removed NPTfm from Integrator.hpp. |
239 |
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|
240 |
|
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Some small syntax cleaning in NPTfm and SimSetup |
241 |
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242 |
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2003-09-22 19:07 tim |
243 |
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244 |
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* libmdtools/: ForceFields.cpp, Integrator.cpp, SimInfo.cpp, |
245 |
|
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SimInfo.hpp: fix bug in calculating maxCutoff |
246 |
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247 |
|
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2003-09-22 17:23 mmeineke |
248 |
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|
249 |
|
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* libmdtools/: AllIntegrator.hpp, Integrator.hpp, Make.dep, |
250 |
|
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Makefile.in, NPT.cpp, NPTf.cpp, NPTfm.cpp, NPTim.cpp, SimSetup.cpp: |
251 |
|
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Converted NPTf to work with the NPT base class. |
252 |
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253 |
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Removed NPTfm and NPTim from cvs |
254 |
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255 |
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2003-09-19 16:00 mmeineke |
256 |
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257 |
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* libmdtools/: AllIntegrator.hpp, Integrator.cpp, Integrator.hpp, |
258 |
|
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NPT.cpp, NPTf.cpp, NPTi.cpp, NVT.cpp, SimSetup.cpp: added NPT base |
259 |
|
|
class. NPTi is up to date. NPTf is not. |
260 |
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261 |
|
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2003-09-19 12:03 mmeineke |
262 |
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263 |
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* utils/Makefile.in, src/Makefile.in: removed mpi++ from the |
264 |
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makefile |
265 |
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266 |
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2003-09-19 12:01 gezelter |
267 |
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268 |
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* samples/water/ssd.bass: goofing off to test NPTf and NPTi |
269 |
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270 |
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2003-09-19 12:01 gezelter |
271 |
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272 |
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* libmdtools/: NPTf.cpp, NPTi.cpp: fixed bugs in NPTf, found |
273 |
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(nearly) conserved quantities for both NPTi and NPTf |
274 |
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275 |
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2003-09-19 11:20 mmeineke |
276 |
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277 |
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* utils/Makefile.in: fixed a typo in the makefile. |
278 |
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279 |
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2003-09-19 10:55 gezelter |
280 |
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281 |
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* libmdtools/NPTi.cpp, libmdtools/SimInfo.cpp, |
282 |
|
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samples/water/ssd.bass: [no log message] |
283 |
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284 |
|
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2003-09-19 10:22 tim |
285 |
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286 |
|
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* libmdtools/: NPTi.cpp, NVT.cpp: [no log message] |
287 |
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288 |
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2003-09-17 10:22 mmeineke |
289 |
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290 |
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* libmdtools/: Integrator.cpp, NPTi.cpp, NVT.cpp: fixed NPTi to now |
291 |
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work with constraints. |
292 |
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293 |
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2003-09-16 16:02 tim |
294 |
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295 |
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* libmdtools/: Integrator.hpp, NPTf.cpp, NPTfm.cpp, NPTi.cpp, |
296 |
|
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SimInfo.cpp, SimInfo.hpp: fixed ecr grow in SimInfo |
297 |
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|
298 |
|
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fixed conserved quantity in NPT (Still some small bug) |
299 |
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300 |
|
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NPTi appears very stable. |
301 |
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302 |
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2003-09-15 12:52 tim |
303 |
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|
304 |
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* libmdtools/AbstractClasses.hpp, libmdtools/Integrator.cpp, |
305 |
|
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libmdtools/Integrator.hpp, libmdtools/NPTf.cpp, |
306 |
|
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libmdtools/NPTfm.cpp, libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, |
307 |
|
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libmdtools/NVT.cpp, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
308 |
|
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libmdtools/StatWriter.cpp, libmdtools/Thermo.cpp, |
309 |
|
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libmdtools/Thermo.hpp, libmdtools/ZConstraint.cpp, |
310 |
|
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utils/sysbuilder/bilayerSys.cpp: add conserved quantity to |
311 |
|
|
statWriter fix bug of vector wrapping at NPTi |
312 |
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313 |
|
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2003-09-12 16:51 mmeineke |
314 |
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|
315 |
|
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* props/: AllCorr.cpp, AllCorr.hpp, GofR.cpp, PairCorrType.cpp, |
316 |
|
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PairCorrType.hpp: added AllCorr. It eill still need some work |
317 |
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318 |
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2003-09-12 12:20 gezelter |
319 |
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320 |
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* libmdtools/: Make.dep, Makefile.in: Added integrators to |
321 |
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Makefile.in |
322 |
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323 |
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2003-09-12 12:20 gezelter |
324 |
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325 |
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* ChangeLog: Entered changes for configure into ChangeLog |
326 |
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327 |
|
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2003-09-10 17:28 mmeineke |
328 |
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|
329 |
gezelter |
760 |
* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added more |
330 |
|
|
work on getting gofR working. |
331 |
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|
332 |
tim |
837 |
2003-09-09 17:50 mmeineke |
333 |
gezelter |
760 |
|
334 |
|
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* props/: GofR.cpp, PairCorrType.cpp, PairCorrType.hpp: added the |
335 |
|
|
beginings of the GofR pair correlation. |
336 |
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|
337 |
|
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added identification of identI in matchI. |
338 |
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|
339 |
tim |
837 |
2003-09-09 16:35 mmeineke |
340 |
gezelter |
760 |
|
341 |
|
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* libmdtools/: Integrator.cpp, Integrator.hpp, NPTxym.cpp, |
342 |
|
|
NPTzm.cpp, Thermo.cpp, Thermo.hpp: updated the ChangeLog |
343 |
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|
344 |
|
|
added two new NPT integrators, they still need work. |
345 |
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|
346 |
tim |
837 |
2003-09-09 16:34 mmeineke |
347 |
gezelter |
760 |
|
348 |
|
|
* ChangeLog: updated the ChangeLog |
349 |
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|
350 |
tim |
837 |
2003-09-05 18:45 gezelter |
351 |
gezelter |
760 |
|
352 |
|
|
* libmdtools/Make.dep: dependency on config.h |
353 |
|
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|
354 |
tim |
837 |
2003-09-05 18:36 gezelter |
355 |
gezelter |
760 |
|
356 |
|
|
* configure, ac-tools/aclocal.m4: fixed sprng problem |
357 |
|
|
|
358 |
tim |
837 |
2003-09-05 17:29 gezelter |
359 |
gezelter |
760 |
|
360 |
|
|
* samples/metals/Makefile.in: New Makefile for metals sample |
361 |
|
|
|
362 |
tim |
837 |
2003-09-05 17:27 gezelter |
363 |
gezelter |
760 |
|
364 |
|
|
* Makefile, Makefile.in, ac-tools/aclocal.m4, |
365 |
|
|
ac-tools/configure.in, ac-tools/fortran90.m4, forceFields/Makefile, |
366 |
|
|
forceFields/Makefile.in, libBASS/Globals.cpp, libBASS/Globals.hpp, |
367 |
|
|
libBASS/MakeStamps.cpp, libBASS/MakeStamps.hpp, libBASS/Makefile, |
368 |
|
|
libBASS/Makefile.in, libmdtools/Integrator.hpp, |
369 |
|
|
libmdtools/Linux_ifc_machdep.F90, libmdtools/Make.dep, |
370 |
|
|
libmdtools/Makefile, libmdtools/Makefile.in, |
371 |
|
|
libmdtools/calc_eam.F90, libmdtools/config.h.in, |
372 |
|
|
libmdtools/definitions_module.F90, libmdtools/fInfo.c, |
373 |
|
|
libmdtools/fortranWrappers.cpp, |
374 |
|
|
libmdtools/mpiSimulation_module.F90, libmdtools/neighborLists.F90, |
375 |
|
|
libmdtools/simulation_module.F90, samples/Makefile, |
376 |
|
|
samples/Makefile.in, samples/alkane/Makefile, |
377 |
|
|
samples/alkane/Makefile.in, samples/argon/Makefile, |
378 |
|
|
samples/argon/Makefile.in, samples/argon/argon.bass, |
379 |
|
|
samples/beadLipid/Makefile, samples/beadLipid/Makefile.in, |
380 |
|
|
samples/lipid/Makefile, samples/lipid/Makefile.in, |
381 |
|
|
samples/water/Makefile, samples/water/Makefile.in, src/Makefile, |
382 |
|
|
src/Makefile.in, utils/Makefile, utils/Makefile.in, |
383 |
|
|
utils/sysbuilder/Makefile, utils/sysbuilder/Makefile.in: Changes to |
384 |
|
|
autoconf / configure method of configuring OOPSE |
385 |
|
|
|
386 |
tim |
837 |
2003-09-04 17:48 mmeineke |
387 |
mmeineke |
754 |
|
388 |
|
|
* libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
389 |
|
|
libmdtools/Makefile, libmdtools/NPTf.cpp, libmdtools/NPTfm.cpp, |
390 |
|
|
libmdtools/NPTi.cpp, libmdtools/NPTim.cpp, libmdtools/NVT.cpp, |
391 |
|
|
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, src/Makefile: |
392 |
|
|
added resetTime to the Global namespace. |
393 |
|
|
|
394 |
|
|
added ability to reset the integrators in the NVT and NPT family. |
395 |
|
|
|
396 |
tim |
837 |
2003-09-04 17:48 mmeineke |
397 |
mmeineke |
754 |
|
398 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: added resetTime to the Global |
399 |
|
|
namespace. |
400 |
|
|
|
401 |
tim |
837 |
2003-09-02 10:30 tim |
402 |
mmeineke |
754 |
|
403 |
|
|
* libmdtools/: Integrator.hpp, Makefile, SimSetup.cpp, |
404 |
|
|
ZConsWriter.cpp, ZConstraint.cpp: fix a bug at MPI version of |
405 |
|
|
PolicyByMass |
406 |
|
|
|
407 |
tim |
837 |
2003-08-28 17:09 tim |
408 |
mmeineke |
754 |
|
409 |
|
|
* ChangeLog, libmdtools/GenericData.cpp, |
410 |
|
|
libmdtools/GenericData.hpp, libmdtools/SimSetup.cpp, |
411 |
|
|
libmdtools/ZConstraint.cpp: Added: check uniqueness of molIndex |
412 |
|
|
|
413 |
tim |
837 |
2003-08-28 12:59 mmeineke |
414 |
mmeineke |
754 |
|
415 |
|
|
* props/: PairCorrType.cpp, PairCorrType.hpp, staticProps.cpp: |
416 |
|
|
added the first functional parts of the PairCorrType Abstract |
417 |
|
|
classes. |
418 |
|
|
|
419 |
tim |
837 |
2003-08-27 15:23 tim |
420 |
tim |
736 |
|
421 |
|
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, ZConstraint.cpp: fix |
422 |
|
|
bug of MPI_Allreduce in ZConstraint, the MPITYPE is set to |
423 |
|
|
MPI_DOUBLE, however, the corret type is MPI_INT. Therefore, when we |
424 |
|
|
turn on the optimization flag, it causes a seg fault |
425 |
|
|
|
426 |
tim |
837 |
2003-08-27 12:25 gezelter |
427 |
tim |
736 |
|
428 |
|
|
* libmdtools/: calc_dipole_dipole.F90, calc_eam.F90, calc_gb.F90, |
429 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90: More fixes for |
430 |
|
|
stress tensor parallel bug. |
431 |
|
|
|
432 |
tim |
837 |
2003-08-27 12:16 tim |
433 |
tim |
736 |
|
434 |
|
|
* ChangeLog, libmdtools/DUFF.cpp, |
435 |
|
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90: |
436 |
|
|
fix bug in calc_dipole_dipole.F90 and calc_stikcy_pair.F90 |
437 |
|
|
molMembershipList use global index instead of local index |
438 |
|
|
|
439 |
tim |
837 |
2003-08-26 16:37 tim |
440 |
tim |
727 |
|
441 |
|
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp, do_Forces.F90, |
442 |
|
|
mpiSimulation.cpp: set default force substraction policy to |
443 |
|
|
PolicyByMass |
444 |
|
|
|
445 |
tim |
837 |
2003-08-26 16:29 tim |
446 |
tim |
727 |
|
447 |
|
|
* libmdtools/Integrator.cpp: [no log message] |
448 |
|
|
|
449 |
tim |
837 |
2003-08-26 16:13 mmeineke |
450 |
tim |
727 |
|
451 |
|
|
* utils/sysbuilder/bilayerSys.cpp: added define statemewnt to |
452 |
|
|
Statwriter and Dumpwriter to handle files larger than 2 gb. |
453 |
|
|
|
454 |
|
|
commented out some print statements in Zconstraint |
455 |
|
|
|
456 |
|
|
hard coding some system init into bilayer.sys |
457 |
|
|
|
458 |
tim |
837 |
2003-08-26 16:12 mmeineke |
459 |
tim |
727 |
|
460 |
|
|
* libmdtools/: DumpWriter.cpp, StatWriter.cpp, ZConstraint.cpp: |
461 |
|
|
added define statemewnt to Statwriter and Dumpwriter to handle |
462 |
|
|
files larger than 2 gb. |
463 |
|
|
|
464 |
|
|
commented out some print statements in Zconstraint |
465 |
|
|
|
466 |
tim |
837 |
2003-08-26 16:02 tim |
467 |
tim |
727 |
|
468 |
|
|
* libmdtools/SimSetup.cpp: Use make_sprng_seed() to generate seed |
469 |
|
|
and check the seed which is specified by user at least contains 9 |
470 |
|
|
digits |
471 |
|
|
|
472 |
tim |
837 |
2003-08-26 14:32 mmeineke |
473 |
tim |
727 |
|
474 |
|
|
* libmdtools/DUFF.cpp: changed the Makefiel a litle. |
475 |
|
|
|
476 |
|
|
Fixed a bug in MPI_DUFF. The atom block type was not being properly |
477 |
|
|
constucted in MPI. (The MPI struct had 6 doubles declared versus |
478 |
|
|
the actual 11) |
479 |
|
|
|
480 |
tim |
837 |
2003-08-26 14:30 mmeineke |
481 |
tim |
727 |
|
482 |
|
|
* Makefile: changed the Makefiel a litle. |
483 |
|
|
|
484 |
tim |
837 |
2003-08-25 18:17 gezelter |
485 |
tim |
727 |
|
486 |
|
|
* utils/sysbuilder/Makefile: More FreeBSD fixes |
487 |
|
|
|
488 |
tim |
837 |
2003-08-25 17:51 gezelter |
489 |
tim |
727 |
|
490 |
|
|
* libBASS/BASSlex.l, libBASS/Makefile, libmdtools/Integrator.hpp, |
491 |
|
|
libmdtools/Makefile, src/Makefile: [no log message] |
492 |
|
|
|
493 |
tim |
837 |
2003-08-22 16:04 mmeineke |
494 |
tim |
727 |
|
495 |
|
|
* libmdtools/: Integrator.cpp, ZConstraint.cpp: small bug fix on |
496 |
|
|
frequency of output dumps. |
497 |
|
|
|
498 |
tim |
837 |
2003-08-20 18:23 tim |
499 |
tim |
727 |
|
500 |
|
|
* libBASS/Globals.hpp, libmdtools/SimInfo.hpp, |
501 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
502 |
|
|
libmdtools/mpiSimulation.cpp: user can setup seed in bass file now, |
503 |
|
|
if he does not specify any value for seed, oopse will take the |
504 |
|
|
value of seconds of system time as seed |
505 |
|
|
|
506 |
tim |
837 |
2003-08-20 15:42 mmeineke |
507 |
tim |
727 |
|
508 |
|
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
509 |
|
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp, |
510 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimState.cpp, |
511 |
|
|
utils/sysbuilder/bilayerSys.cpp: updated the Changelog. |
512 |
|
|
|
513 |
|
|
added some bug fixes for setting the random number generator seed |
514 |
|
|
value. |
515 |
|
|
|
516 |
|
|
fixed a bug where ghostbend atom b was not being set. ( recent bug |
517 |
|
|
from SimState conversion) |
518 |
|
|
|
519 |
tim |
837 |
2003-08-20 15:41 mmeineke |
520 |
tim |
727 |
|
521 |
|
|
* libBASS/Globals.hpp: updated the Changelog. |
522 |
|
|
|
523 |
|
|
added some bug fixes for setting the random number generator seed |
524 |
|
|
value. |
525 |
|
|
|
526 |
tim |
837 |
2003-08-20 15:41 mmeineke |
527 |
tim |
727 |
|
528 |
|
|
* ChangeLog: updated the Changelog. |
529 |
|
|
|
530 |
tim |
837 |
2003-08-20 15:11 tim |
531 |
tim |
727 |
|
532 |
|
|
* libBASS/Globals.cpp, libmdtools/DUFF.cpp, |
533 |
|
|
libmdtools/GhostBend.cpp, libmdtools/SRI.hpp: bug fixed in ghost |
534 |
|
|
bend class |
535 |
|
|
|
536 |
tim |
837 |
2003-08-20 11:13 mmeineke |
537 |
tim |
727 |
|
538 |
|
|
* utils/: Makefile, sysbuilder/Makefile: quick makefile fix, in |
539 |
|
|
make links. added -f to ln -s. |
540 |
|
|
|
541 |
tim |
837 |
2003-08-20 10:50 tim |
542 |
tim |
727 |
|
543 |
|
|
* libmdtools/: ZConsWriter.cpp, ZConstraint.cpp: [no log message] |
544 |
|
|
|
545 |
tim |
837 |
2003-08-20 10:34 tim |
546 |
tim |
727 |
|
547 |
|
|
* libmdtools/: Integrator.hpp, SimSetup.cpp, ZConsWriter.cpp, |
548 |
|
|
ZConstraint.cpp: reformmating ZConstraint and fixe bug of error msg |
549 |
|
|
printing |
550 |
|
|
|
551 |
tim |
837 |
2003-08-18 16:59 chuckv |
552 |
mmeineke |
705 |
|
553 |
|
|
* utils/sysbuilder/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
554 |
|
|
latticeBuilder.cpp, latticeBuilder.hpp, nanoBuilder.cpp, |
555 |
|
|
sysBuild.cpp, sysBuild.hpp: Fixed sysBuild -bilayer works. |
556 |
|
|
Nanobuilder still broke. |
557 |
|
|
|
558 |
tim |
837 |
2003-08-15 15:24 tim |
559 |
mmeineke |
705 |
|
560 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
561 |
|
|
libmdtools/GenericData.hpp, libmdtools/Integrator.hpp, |
562 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp, |
563 |
|
|
libmdtools/ZConsWriter.cpp, libmdtools/ZConsWriter.hpp, |
564 |
|
|
libmdtools/ZConstraint.cpp: Tested MPI version of Z-Constraint |
565 |
|
|
Method |
566 |
|
|
|
567 |
tim |
837 |
2003-08-14 12:16 tim |
568 |
mmeineke |
705 |
|
569 |
|
|
* libmdtools/: Integrator.hpp, ZConstraint.cpp: Stable ZConstraint |
570 |
|
|
with average force substraction strategy |
571 |
|
|
|
572 |
tim |
837 |
2003-08-13 17:20 chuckv |
573 |
mmeineke |
705 |
|
574 |
|
|
* libmdtools/: do_Forces.F90, mpiSimulation_module.F90: Added some |
575 |
|
|
profiling code -DPROFILE. |
576 |
|
|
|
577 |
tim |
837 |
2003-08-13 15:21 tim |
578 |
mmeineke |
705 |
|
579 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
580 |
|
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
581 |
|
|
libmdtools/SimSetup.cpp, libmdtools/ZConstraint.cpp: harmonic |
582 |
|
|
potential & z-contraint method |
583 |
|
|
|
584 |
tim |
837 |
2003-08-12 17:44 mmeineke |
585 |
mmeineke |
705 |
|
586 |
|
|
* libBASS/BASS_interface.cpp, libBASS/Globals.hpp, |
587 |
|
|
libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
588 |
|
|
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
589 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimSetup.cpp: fixed a really |
590 |
|
|
annoying bug in Directional Atom, where mu was getting written to |
591 |
|
|
pseudorandom memory location. |
592 |
|
|
|
593 |
tim |
837 |
2003-08-12 15:56 tim |
594 |
mmeineke |
705 |
|
595 |
|
|
* libBASS/BASS_interface.cpp, libBASS/Globals.cpp, |
596 |
|
|
libBASS/Globals.hpp, libmdtools/Atom.hpp, |
597 |
|
|
libmdtools/DirectionalAtom.cpp, libmdtools/InitializeFromFile.cpp, |
598 |
|
|
libmdtools/SimSetup.cpp: debugging globals |
599 |
|
|
|
600 |
tim |
837 |
2003-08-12 14:40 gezelter |
601 |
mmeineke |
705 |
|
602 |
|
|
* forceFields/: DUFF.frc, EAM_FF.frc, LJFF.frc: formatting fixes |
603 |
|
|
and new atypes in LJFF |
604 |
|
|
|
605 |
tim |
837 |
2003-08-12 14:15 gezelter |
606 |
mmeineke |
705 |
|
607 |
|
|
* forceFields/: DUFF.frc, LJFF.frc: fixed a few references to older |
608 |
|
|
stuff... |
609 |
|
|
|
610 |
tim |
837 |
2003-08-12 14:14 chuckv |
611 |
mmeineke |
705 |
|
612 |
|
|
* utils/sysbuilder/sysBuild.ggo: Added comment line for getgetopt. |
613 |
|
|
|
614 |
tim |
837 |
2003-08-12 14:04 chuckv |
615 |
mmeineke |
705 |
|
616 |
|
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp: |
617 |
|
|
Missed del of files before. |
618 |
|
|
|
619 |
tim |
837 |
2003-08-12 14:03 chuckv |
620 |
mmeineke |
705 |
|
621 |
|
|
* utils/sysbuilder/: MPIobj/placeHolder, obj/placeHolder: [no log |
622 |
|
|
message] |
623 |
|
|
|
624 |
tim |
837 |
2003-08-12 14:01 chuckv |
625 |
mmeineke |
705 |
|
626 |
|
|
* utils/sysbuilder/Makefile: commit makefile |
627 |
|
|
|
628 |
tim |
837 |
2003-08-12 13:51 tim |
629 |
mmeineke |
705 |
|
630 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
631 |
|
|
libmdtools/GenericData.cpp, libmdtools/GenericData.hpp, |
632 |
|
|
libmdtools/Integrator.hpp, libmdtools/SimSetup.cpp, |
633 |
|
|
libmdtools/SimSetup.hpp, libmdtools/ZConstraint.cpp: added |
634 |
|
|
harmonical potential to z-constraint method |
635 |
|
|
|
636 |
tim |
837 |
2003-08-11 18:31 chuckv |
637 |
mmeineke |
705 |
|
638 |
|
|
* utils/Makefile: Changed makefile to only build quicklate. |
639 |
|
|
|
640 |
tim |
837 |
2003-08-11 18:25 chuckv |
641 |
mmeineke |
705 |
|
642 |
|
|
* ac-tools/configure.in: added utils/sysbuilder to be built. |
643 |
|
|
|
644 |
tim |
837 |
2003-08-11 18:12 chuckv |
645 |
mmeineke |
705 |
|
646 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
647 |
|
|
bilayerSys.hpp, latticeBuilder.cpp, latticeBuilder.hpp, |
648 |
|
|
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp, sysbuilder/MoLocator.cpp, |
649 |
|
|
sysbuilder/MoLocator.hpp, sysbuilder/bilayerSys.cpp, |
650 |
|
|
sysbuilder/bilayerSys.hpp, sysbuilder/cmdline.c, |
651 |
|
|
sysbuilder/cmdline.h, sysbuilder/latticeBuilder.cpp, |
652 |
|
|
sysbuilder/latticeBuilder.hpp, sysbuilder/nanoBuilder.cpp, |
653 |
|
|
sysbuilder/nanoBuilder.hpp, sysbuilder/sysBuild.cpp, |
654 |
|
|
sysbuilder/sysBuild.ggo, sysbuilder/sysBuild.hpp: Arranged |
655 |
|
|
sysbuilder into a subdirectory. Fixed some of sysbuilder to work |
656 |
|
|
with new atom allocation in libmdtools. |
657 |
|
|
|
658 |
tim |
837 |
2003-08-11 15:41 tim |
659 |
mmeineke |
705 |
|
660 |
|
|
* libmdtools/: Integrator.cpp, Integrator.hpp: added method of |
661 |
|
|
moving zconstraint molecules to specified positions |
662 |
|
|
|
663 |
tim |
837 |
2003-08-11 15:39 tim |
664 |
mmeineke |
705 |
|
665 |
|
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: [no log message] |
666 |
|
|
|
667 |
tim |
837 |
2003-08-11 15:38 mmeineke |
668 |
mmeineke |
705 |
|
669 |
|
|
* libBASS/BASS_interface.cpp, libBASS/BASS_interface.h, |
670 |
|
|
libBASS/BASS_parse.c, libBASS/BASSyacc.y, libBASS/Globals.cpp, |
671 |
|
|
libBASS/Globals.hpp, libBASS/Makefile, libBASS/ZconStamp.cpp, |
672 |
|
|
libBASS/ZconStamp.hpp, libBASS/interface.c, libBASS/make_nodes.c, |
673 |
|
|
libBASS/make_nodes.h, libBASS/mpiBASS.c, libBASS/mpiBASS.h, |
674 |
|
|
libBASS/node_list.h, libBASS/parse_interface.h, |
675 |
|
|
libBASS/parse_tree.c, libmdtools/SimInfo.hpp: Added zConstraint |
676 |
|
|
into the BASS language syntax. |
677 |
|
|
|
678 |
tim |
837 |
2003-08-11 14:29 mmeineke |
679 |
mmeineke |
705 |
|
680 |
|
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp: changed the number of |
681 |
|
|
degrees of freedom to account for zConstreints |
682 |
|
|
|
683 |
tim |
837 |
2003-08-08 17:22 chuckv |
684 |
mmeineke |
705 |
|
685 |
|
|
* libmdtools/EAM_FF.cpp, libmdtools/calc_eam.F90, |
686 |
|
|
libmdtools/do_Forces.F90, libmdtools/neighborLists.F90, |
687 |
|
|
samples/metals/Au.bass: EAM works...... Neighbor list also |
688 |
|
|
works..... |
689 |
|
|
|
690 |
tim |
837 |
2003-08-08 14:32 mmeineke |
691 |
mmeineke |
705 |
|
692 |
|
|
* props/: frameCount.c, frameCount.h, props.cpp, staticProps.cpp: |
693 |
|
|
moved frameCount's functionality into DumpReader. also split props |
694 |
|
|
into staticProps and dynamicProps. (currently only have |
695 |
|
|
staticProps) |
696 |
|
|
|
697 |
tim |
837 |
2003-08-08 13:48 mmeineke |
698 |
mmeineke |
705 |
|
699 |
|
|
* libmdtools/: Makefile, ZConstraint.cpp: fixed a deprcated |
700 |
|
|
instance of Atom::setZ and Atom::getZ in ZConstaint. |
701 |
|
|
|
702 |
tim |
837 |
2003-08-07 17:47 mmeineke |
703 |
mmeineke |
705 |
|
704 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, Bend.cpp, Bond.cpp, |
705 |
|
|
DirectionalAtom.cpp, DumpWriter.cpp, ForceFields.cpp, |
706 |
|
|
GhostBend.cpp, InitializeFromFile.cpp, Makefile, SimInfo.cpp, |
707 |
|
|
SimInfo.hpp, SimSetup.cpp, SimSetup.hpp, SimState.cpp, |
708 |
|
|
SimState.hpp, Torsion.cpp: switched SimInfo to use a system |
709 |
|
|
configuration from SimState rather than arrays from Atom |
710 |
|
|
|
711 |
tim |
837 |
2003-08-06 20:47 chuckv |
712 |
mmeineke |
705 |
|
713 |
|
|
* libmdtools/Atom.hpp, libmdtools/EAM_FF.cpp, |
714 |
|
|
libmdtools/SimInfo.cpp, libmdtools/calc_eam.F90, |
715 |
|
|
libmdtools/do_Forces.F90, libmdtools/notifyCutoffs.F90, |
716 |
|
|
samples/metals/Au.bass: Bug fixes for eam... |
717 |
|
|
|
718 |
tim |
837 |
2003-08-01 12:18 tim |
719 |
mmeineke |
705 |
|
720 |
|
|
* libmdtools/: SimSetup.cpp, ZConstraint.cpp: stable version of |
721 |
|
|
Z-Constraint |
722 |
|
|
|
723 |
tim |
837 |
2003-07-31 15:59 tim |
724 |
mmeineke |
705 |
|
725 |
|
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
726 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
727 |
|
|
libmdtools/ZConstraint.cpp: add index range checking into |
728 |
|
|
ZConstraint |
729 |
|
|
|
730 |
tim |
837 |
2003-07-31 11:38 tim |
731 |
tim |
660 |
|
732 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: added z-constraint parameters |
733 |
|
|
to the globals |
734 |
|
|
|
735 |
tim |
837 |
2003-07-31 11:35 tim |
736 |
tim |
660 |
|
737 |
|
|
* libmdtools/: AllIntegrator.hpp, GenericData.cpp, GenericData.hpp, |
738 |
|
|
Integrator.hpp, Makefile, Molecule.cpp, Molecule.hpp, NPTf.cpp, |
739 |
|
|
NPTfm.cpp, NPTi.cpp, NPTim.cpp, NVT.cpp, SimInfo.cpp, SimInfo.hpp, |
740 |
|
|
SimSetup.cpp, ZConsWriter.cpp, ZConsWriter.hpp, ZConstraint.cpp: |
741 |
|
|
Added Z constraint. |
742 |
|
|
|
743 |
tim |
837 |
2003-07-30 17:17 chuckv |
744 |
tim |
660 |
|
745 |
mmeineke |
705 |
* libmdtools/EAM_FF.cpp, libmdtools/ForceFields.hpp, |
746 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/calc_eam.F90, |
747 |
|
|
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, |
748 |
|
|
samples/metals/Au.bass: More bug fixes for eam. |
749 |
tim |
660 |
|
750 |
tim |
837 |
2003-07-29 12:32 mmeineke |
751 |
tim |
660 |
|
752 |
|
|
* libmdtools/DumpReader.cpp, libmdtools/ReadWrite.hpp, |
753 |
mmeineke |
705 |
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
754 |
|
|
props/frameCount.c, props/frameCount.h, props/props.cpp, |
755 |
|
|
src/Makefile: working on the props code |
756 |
tim |
660 |
|
757 |
tim |
837 |
2003-07-29 12:32 mmeineke |
758 |
tim |
660 |
|
759 |
|
|
* libBASS/Globals.cpp: [no log message] |
760 |
|
|
|
761 |
tim |
837 |
2003-07-25 16:05 chuckv |
762 |
mmeineke |
705 |
|
763 |
|
|
* samples/metals/: Au.bass, metals.mdl: Added bass models for |
764 |
|
|
metals |
765 |
|
|
|
766 |
tim |
837 |
2003-07-25 16:00 chuckv |
767 |
tim |
660 |
|
768 |
|
|
* libmdtools/: Makefile, SimSetup.cpp, calc_eam.F90, |
769 |
|
|
notifyCutoffs.F90: Added eam to simSetup and added changecutoffeam. |
770 |
|
|
|
771 |
tim |
837 |
2003-07-24 17:22 chuckv |
772 |
tim |
660 |
|
773 |
|
|
* ac-tools/configure.in: Changed configure to look for both upper |
774 |
|
|
and lower cass .mod files |
775 |
|
|
|
776 |
tim |
837 |
2003-07-24 15:57 chuckv |
777 |
tim |
660 |
|
778 |
|
|
* libmdtools/: calc_eam.F90, do_Forces.F90: module use fixes for |
779 |
|
|
eam and do_forces. |
780 |
|
|
|
781 |
tim |
837 |
2003-07-23 18:13 chuckv |
782 |
tim |
660 |
|
783 |
|
|
* libmdtools/: Makefile, calc_eam.F90, do_Forces.F90, |
784 |
|
|
force_globals.F90, simulation_module.F90, status_module.F90: |
785 |
|
|
Finished most code for eam.... |
786 |
|
|
|
787 |
tim |
837 |
2003-07-22 17:49 mmeineke |
788 |
tim |
660 |
|
789 |
|
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: added the scan |
790 |
|
|
function to the DumpReader. It should now save the start of each |
791 |
|
|
frame in a vector. |
792 |
|
|
|
793 |
tim |
837 |
2003-07-22 16:05 mmeineke |
794 |
tim |
660 |
|
795 |
|
|
* libmdtools/: DumpReader.cpp, ReadWrite.hpp: making some changes |
796 |
|
|
to read dump files |
797 |
|
|
|
798 |
tim |
837 |
2003-07-22 15:54 tim |
799 |
tim |
660 |
|
800 |
|
|
* libmdtools/: AbstractClasses.hpp, AllIntegrator.hpp, |
801 |
|
|
Integrator.cpp, Integrator.hpp, Makefile, NPTf.cpp, NPTfm.cpp, |
802 |
|
|
NPTi.cpp, NPTim.cpp, NVT.cpp, SimSetup.cpp, SimSetup.hpp: [no log |
803 |
|
|
message] |
804 |
|
|
|
805 |
tim |
837 |
2003-07-22 12:41 mmeineke |
806 |
tim |
660 |
|
807 |
|
|
* libmdtools/: InitializeFromFile.cpp, ReadWrite.hpp, SimInfo.hpp, |
808 |
|
|
SimSetup.cpp: Fixed a current time initialization bug in |
809 |
|
|
InitFromFile. |
810 |
|
|
|
811 |
tim |
837 |
2003-07-21 17:27 mmeineke |
812 |
tim |
660 |
|
813 |
|
|
* libmdtools/: DumpReader.cpp, InitializeFromFile.cpp, |
814 |
|
|
Integrator.cpp, SimInfo.hpp: some initial changes to Dumpwriter and |
815 |
|
|
friends to accomadate random file access |
816 |
|
|
|
817 |
tim |
837 |
2003-07-21 12:23 mmeineke |
818 |
tim |
660 |
|
819 |
|
|
* libmdtools/SimInfo.cpp: Initialized currentTime to 0, in case no |
820 |
|
|
one sets it. |
821 |
|
|
|
822 |
tim |
837 |
2003-07-21 12:23 mmeineke |
823 |
tim |
660 |
|
824 |
|
|
* libmdtools/: InitializeFromFile.cpp, Integrator.cpp, |
825 |
|
|
ReadWrite.hpp: fixed Initializefrom file to start the simulation |
826 |
|
|
from the time specified in the init file. |
827 |
|
|
|
828 |
tim |
837 |
2003-07-17 17:49 gezelter |
829 |
tim |
660 |
|
830 |
|
|
* libmdtools/: Integrator.cpp, ReadWrite.hpp, SimInfo.hpp, |
831 |
|
|
DumpReader.cpp: Started work on a DumpReader |
832 |
|
|
|
833 |
tim |
837 |
2003-07-17 16:38 gezelter |
834 |
tim |
660 |
|
835 |
|
|
* libmdtools/calc_sticky_pair.F90: Fixes for SSD/E |
836 |
|
|
|
837 |
tim |
837 |
2003-07-17 16:32 gezelter |
838 |
tim |
660 |
|
839 |
|
|
* forceFields/DUFF.frc, libmdtools/DUFF.cpp, |
840 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/fortranWrapDefines.hpp: |
841 |
|
|
Changes for SSD/E |
842 |
|
|
|
843 |
tim |
837 |
2003-07-17 15:38 mmeineke |
844 |
tim |
660 |
|
845 |
|
|
* libmdtools/do_Forces.F90: commented out an eam line |
846 |
|
|
|
847 |
tim |
837 |
2003-07-17 15:32 chuckv |
848 |
tim |
660 |
|
849 |
|
|
* libmdtools/atype_module.F90: fixed spelling issue |
850 |
|
|
|
851 |
tim |
837 |
2003-07-17 15:29 chuckv |
852 |
tim |
660 |
|
853 |
|
|
* libmdtools/: fInfo.c, status_module.F90: added info module |
854 |
|
|
|
855 |
tim |
837 |
2003-07-17 15:25 chuckv |
856 |
tim |
660 |
|
857 |
|
|
* libmdtools/: Atom.hpp, DUFF.cpp, EAM_FF.cpp, LJFF.cpp, Makefile, |
858 |
|
|
atype_module.F90, calc_eam.F90, do_Forces.F90, |
859 |
|
|
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
860 |
|
|
mpiSimulation_module.F90: Added massive changes for eam.... |
861 |
|
|
|
862 |
tim |
837 |
2003-07-16 17:49 chuckv |
863 |
tim |
660 |
|
864 |
|
|
* libmdtools/EAM_FF.cpp: More up to date version of EAM_FF |
865 |
|
|
|
866 |
tim |
837 |
2003-07-16 17:30 mmeineke |
867 |
tim |
660 |
|
868 |
|
|
* libmdtools/: ForceFields.cpp, Makefile, SimInfo.cpp, SimInfo.hpp, |
869 |
|
|
SimSetup.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
870 |
|
|
calc_reaction_field.F90, do_Forces.F90, fSimulation.h, |
871 |
|
|
fortranWrapDefines.hpp, fortranWrappers.cpp, fortranWrappers.hpp, |
872 |
|
|
neighborLists.F90, notifyCutoffs.F90, simulation_module.F90, |
873 |
|
|
wrappers.F90: Changed how cutoffs were handled from C. Now |
874 |
|
|
notifyCutoffs in Fortran notifies those who need the information of |
875 |
|
|
any changes to cutoffs. |
876 |
|
|
|
877 |
tim |
837 |
2003-07-16 13:35 gezelter |
878 |
tim |
660 |
|
879 |
|
|
* utils/: Makefile, quickLate.c: Made quickLate aware of Hmat. |
880 |
|
|
quickLate is now somewhat more intelligent about periodic |
881 |
|
|
boundaries and wrapping. |
882 |
|
|
|
883 |
tim |
837 |
2003-07-16 12:40 chuckv |
884 |
tim |
660 |
|
885 |
|
|
* libmdtools/calc_LJ_FF.F90: Fixed bug in updating mixing lists |
886 |
|
|
|
887 |
tim |
837 |
2003-07-16 11:34 mmeineke |
888 |
tim |
660 |
|
889 |
|
|
* scripts/cleanSrc: added a quick wipe-and-update script for quick |
890 |
|
|
rebuilds on BoB |
891 |
|
|
|
892 |
tim |
837 |
2003-07-15 22:11 gezelter |
893 |
tim |
660 |
|
894 |
|
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimInfo.hpp, |
895 |
|
|
SimSetup.cpp, calc_dipole_dipole.F90, calc_reaction_field.F90: more |
896 |
|
|
fixes for box changes |
897 |
|
|
|
898 |
tim |
837 |
2003-07-15 18:29 mmeineke |
899 |
tim |
660 |
|
900 |
|
|
* libmdtools/simulation_module.F90: removed some debugging print |
901 |
|
|
statements. |
902 |
|
|
|
903 |
tim |
837 |
2003-07-15 18:22 mmeineke |
904 |
tim |
660 |
|
905 |
|
|
* libmdtools/: SimInfo.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
906 |
|
|
do_Forces.F90, simulation_module.F90: fixed a long lived bug in |
907 |
|
|
do_forces. Rrf was not being used in the neighborlist correctly. |
908 |
|
|
rcut was conssistently being set lowere than Rrf causing the dipole |
909 |
|
|
cutoff region to be to small. Also led to the removal of the taper |
910 |
|
|
region to buffer the dipole cutoff. |
911 |
|
|
|
912 |
tim |
837 |
2003-07-15 17:34 mmeineke |
913 |
tim |
660 |
|
914 |
|
|
* libmdtools/: SimInfo.cpp, simulation_module.F90: working on |
915 |
|
|
fixing ssd bug |
916 |
|
|
|
917 |
tim |
837 |
2003-07-15 15:56 gezelter |
918 |
tim |
660 |
|
919 |
|
|
* libmdtools/: NPTf.cpp, NPTfm.cpp, NPTi.cpp, SimInfo.cpp: Fixes |
920 |
|
|
for the NPT ensembles |
921 |
|
|
|
922 |
tim |
837 |
2003-07-15 14:52 mmeineke |
923 |
tim |
660 |
|
924 |
|
|
* libmdtools/: Makefile, SimSetup.cpp, SimSetup.hpp: cleaned up |
925 |
|
|
simSetup |
926 |
|
|
|
927 |
tim |
837 |
2003-07-15 13:57 mmeineke |
928 |
tim |
660 |
|
929 |
|
|
* libmdtools/: Integrator.cpp, NPTi.cpp, SRI.hpp, SimSetup.cpp, |
930 |
|
|
SimSetup.hpp, Thermo.cpp, Thermo.hpp, f_verlet_constrained.F90: |
931 |
|
|
fixed some bugs, Changed entry_plug to info where appropriate |
932 |
|
|
|
933 |
tim |
837 |
2003-07-15 13:25 chuckv |
934 |
tim |
660 |
|
935 |
|
|
* utils/sysBuild.ggo: added more command line arguments |
936 |
|
|
|
937 |
tim |
837 |
2003-07-15 13:11 gezelter |
938 |
tim |
660 |
|
939 |
|
|
* samples/: alkane/butane.bass, lipid/5x5.bass, water/ssd.bass: |
940 |
|
|
Fixing force field line |
941 |
|
|
|
942 |
tim |
837 |
2003-07-15 13:10 gezelter |
943 |
tim |
660 |
|
944 |
|
|
* libmdtools/: Atom.hpp, NPTi.cpp, NPTim.cpp, Thermo.cpp, |
945 |
|
|
calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
946 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90: Fixing pressure |
947 |
|
|
tensor |
948 |
|
|
|
949 |
tim |
837 |
2003-07-15 11:50 gezelter |
950 |
tim |
660 |
|
951 |
|
|
* libmdtools/: Bond.cpp, Molecule.cpp: more archaic code fixes |
952 |
|
|
|
953 |
tim |
837 |
2003-07-15 11:42 gezelter |
954 |
tim |
660 |
|
955 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, Verlet.cpp: |
956 |
|
|
removed old outdated code |
957 |
|
|
|
958 |
tim |
837 |
2003-07-15 10:45 gezelter |
959 |
tim |
660 |
|
960 |
|
|
* libmdtools/Thermo.cpp: fixes to get rid of get_vx and set_vx |
961 |
|
|
|
962 |
tim |
837 |
2003-07-15 10:28 gezelter |
963 |
tim |
660 |
|
964 |
|
|
* libmdtools/Molecule.cpp: removing get_vx |
965 |
|
|
|
966 |
tim |
837 |
2003-07-14 23:28 gezelter |
967 |
tim |
660 |
|
968 |
|
|
* libmdtools/NPTfm.cpp: Added NPTfm |
969 |
|
|
|
970 |
tim |
837 |
2003-07-14 23:27 gezelter |
971 |
tim |
660 |
|
972 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
973 |
|
|
Bugfix in NPTim, fixes for NPTfm |
974 |
|
|
|
975 |
tim |
837 |
2003-07-14 23:08 gezelter |
976 |
tim |
660 |
|
977 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp, SimSetup.cpp: |
978 |
|
|
Checking in changes for NPTim |
979 |
|
|
|
980 |
tim |
837 |
2003-07-14 19:06 gezelter |
981 |
tim |
660 |
|
982 |
|
|
* utils/Makefile: Broken SysBuilder |
983 |
|
|
|
984 |
tim |
837 |
2003-07-14 19:06 gezelter |
985 |
tim |
660 |
|
986 |
|
|
* samples/: alkane/init_butane.eor, argon/argon.bass, |
987 |
|
|
argon/init_argon.eor, lipid/init_5x5.eor, water/init_ssd.eor: Fixes |
988 |
|
|
for samples |
989 |
|
|
|
990 |
tim |
837 |
2003-07-14 19:06 gezelter |
991 |
tim |
660 |
|
992 |
|
|
* libmdtools/: Integrator.cpp, do_Forces.F90: Removed some |
993 |
|
|
debugging write statements |
994 |
|
|
|
995 |
tim |
837 |
2003-07-14 18:38 gezelter |
996 |
tim |
660 |
|
997 |
|
|
* libmdtools/: Integrator.cpp, Integrator.hpp, NPTf.cpp, NPTi.cpp, |
998 |
|
|
NVT.cpp: Fixes for get and set routines in Atom and DirectionalAtom |
999 |
|
|
|
1000 |
tim |
837 |
2003-07-14 17:48 mmeineke |
1001 |
tim |
660 |
|
1002 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, DirectionalAtom.cpp: added get |
1003 |
|
|
and set routines to Atom and DirectionalAtom |
1004 |
|
|
|
1005 |
tim |
837 |
2003-07-14 17:35 chuckv |
1006 |
tim |
660 |
|
1007 |
|
|
* utils/: nanoBuilder.cpp, nanoBuilder.hpp, nanoSysBuild.cpp, |
1008 |
|
|
sysBuild.cpp, sysBuild.ggo, sysBuild.hpp: added a nanoSysBuilder |
1009 |
|
|
that takes different cmd line arguments. |
1010 |
|
|
|
1011 |
tim |
837 |
2003-07-14 17:28 mmeineke |
1012 |
tim |
660 |
|
1013 |
|
|
* libmdtools/: Atom.hpp, BondExtensions.cpp, DirectionalAtom.cpp, |
1014 |
|
|
ForceFields.cpp, Integrator.cpp, Integrator.hpp, Makefile, |
1015 |
|
|
SimInfo.cpp, SimInfo.hpp, do_Forces.F90: found a bug. Unit vectors |
1016 |
|
|
were not being updated |
1017 |
|
|
|
1018 |
tim |
837 |
2003-07-14 11:04 gezelter |
1019 |
tim |
660 |
|
1020 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTim.cpp: Working on |
1021 |
|
|
NPTim |
1022 |
|
|
|
1023 |
tim |
837 |
2003-07-14 10:55 mmeineke |
1024 |
tim |
660 |
|
1025 |
|
|
* forceFields/DUFF.frc: Switched the bond in the force field back |
1026 |
|
|
to constrained, to preserve energy |
1027 |
|
|
|
1028 |
tim |
837 |
2003-07-11 18:34 mmeineke |
1029 |
tim |
660 |
|
1030 |
|
|
* libmdtools/: BondExtensions.cpp, DUFF.cpp, Integrator.cpp, |
1031 |
|
|
Integrator.hpp: working on som integrator bugs |
1032 |
|
|
|
1033 |
tim |
837 |
2003-07-11 11:26 gezelter |
1034 |
tim |
660 |
|
1035 |
|
|
* libmdtools/: StreamTokenizer.cpp, StreamTokenizer.hpp: Starting |
1036 |
|
|
to worry about all the strtok() calls in our code |
1037 |
|
|
|
1038 |
tim |
837 |
2003-07-11 10:49 gezelter |
1039 |
tim |
660 |
|
1040 |
|
|
* utils/nanoBuilder.cpp: Fixed Hmat and some namespace strangeness |
1041 |
|
|
|
1042 |
tim |
837 |
2003-07-10 21:15 gezelter |
1043 |
tim |
660 |
|
1044 |
|
|
* libmdtools/DumpWriter.cpp: Fixed hmat in DumpWriter (MPI) and |
1045 |
|
|
eor. |
1046 |
|
|
|
1047 |
tim |
837 |
2003-07-10 18:15 mmeineke |
1048 |
tim |
660 |
|
1049 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, NPTf.cpp, |
1050 |
|
|
SimInfo.cpp, Thermo.cpp: fixed some bugs |
1051 |
|
|
|
1052 |
tim |
837 |
2003-07-10 15:53 chuckv |
1053 |
tim |
660 |
|
1054 |
|
|
* utils/: Makefile, latticeBuilder.cpp, latticeBuilder.hpp, |
1055 |
|
|
nanoBuilder.cpp, nanoBuilder.hpp, sysBuild.cpp, sysBuild.hpp: Added |
1056 |
|
|
nanoBuilder and a general Lattice builder. |
1057 |
|
|
|
1058 |
tim |
837 |
2003-07-10 13:10 gezelter |
1059 |
tim |
660 |
|
1060 |
|
|
* libmdtools/: Integrator.hpp, NPTf.cpp, SimInfo.cpp, SimInfo.hpp, |
1061 |
|
|
Thermo.cpp, Thermo.hpp: Bunch of 1-d array -> 2-d array stuff |
1062 |
|
|
|
1063 |
tim |
837 |
2003-07-09 18:14 mmeineke |
1064 |
tim |
660 |
|
1065 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
1066 |
|
|
Integrator.hpp, NPTf.cpp, NPTi.cpp, ReadWrite.hpp, SimInfo.cpp, |
1067 |
|
|
SimSetup.cpp: Bug fixing NPTi and NPTf. there is some error in the |
1068 |
|
|
caclulation of HmatInverse. |
1069 |
|
|
|
1070 |
tim |
837 |
2003-07-09 11:34 mmeineke |
1071 |
tim |
660 |
|
1072 |
|
|
* libBASS/MoleculeStamp.hpp: starting some work for xlate |
1073 |
|
|
|
1074 |
tim |
837 |
2003-07-09 11:33 mmeineke |
1075 |
tim |
660 |
|
1076 |
|
|
* libmdtools/: SimSetup.cpp, Thermo.cpp: adding in dan's NPT stuff |
1077 |
|
|
|
1078 |
tim |
837 |
2003-07-09 09:56 gezelter |
1079 |
tim |
660 |
|
1080 |
|
|
* libmdtools/: NPTf.cpp, SimSetup.cpp: Fixes and merging NPTf |
1081 |
|
|
|
1082 |
tim |
837 |
2003-07-09 09:56 gezelter |
1083 |
tim |
660 |
|
1084 |
|
|
* libBASS/Globals.cpp: Removed Qmass |
1085 |
|
|
|
1086 |
tim |
837 |
2003-07-08 22:15 gezelter |
1087 |
tim |
660 |
|
1088 |
|
|
* libmdtools/: Makefile, NPTf.cpp, NPTi.cpp: Fixes for both NPTf |
1089 |
|
|
and NPTi |
1090 |
|
|
|
1091 |
tim |
837 |
2003-07-08 21:41 gezelter |
1092 |
tim |
660 |
|
1093 |
|
|
* libmdtools/: NPTf.cpp, NPTi.cpp: Fixes in NPTi migrated into NPTf |
1094 |
|
|
|
1095 |
tim |
837 |
2003-07-08 17:10 gezelter |
1096 |
tim |
660 |
|
1097 |
|
|
* libmdtools/: Integrator.hpp, NPTf.cpp: [no log message] |
1098 |
|
|
|
1099 |
tim |
837 |
2003-07-08 17:06 gezelter |
1100 |
tim |
660 |
|
1101 |
|
|
* libmdtools/NPTi.cpp: fixed box scaling |
1102 |
|
|
|
1103 |
tim |
837 |
2003-07-08 16:56 gezelter |
1104 |
tim |
660 |
|
1105 |
|
|
* libmdtools/: Integrator.hpp, Makefile, NPTi.cpp, SimInfo.cpp, |
1106 |
|
|
SimInfo.hpp, Thermo.cpp: NPTi |
1107 |
|
|
|
1108 |
tim |
837 |
2003-07-03 15:41 mmeineke |
1109 |
tim |
660 |
|
1110 |
|
|
* libBASS/Makefile, libmdtools/Makefile, src/Makefile, |
1111 |
|
|
utils/Makefile, utils/bilayerSys.cpp: cleaned up the dependecy |
1112 |
|
|
scripts in the makefiles |
1113 |
|
|
|
1114 |
tim |
837 |
2003-07-02 17:26 mmeineke |
1115 |
tim |
660 |
|
1116 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
1117 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
1118 |
|
|
libmdtools/Makefile, libmdtools/ReadWrite.hpp, |
1119 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1120 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1121 |
|
|
libmdtools/do_Forces.F90, libmdtools/wrappers.F90, src/Makefile, |
1122 |
|
|
utils/Makefile: fixed the bugs introduced by switching the periodic |
1123 |
|
|
box to a matrix |
1124 |
|
|
|
1125 |
tim |
837 |
2003-07-01 18:39 gezelter |
1126 |
tim |
660 |
|
1127 |
|
|
* libmdtools/do_Forces.F90: Fortran flexi-BOX |
1128 |
|
|
|
1129 |
tim |
837 |
2003-07-01 18:29 gezelter |
1130 |
tim |
660 |
|
1131 |
|
|
* libmdtools/simulation_module.F90: Fixes for flexi-BOX |
1132 |
|
|
|
1133 |
tim |
837 |
2003-07-01 17:33 mmeineke |
1134 |
tim |
660 |
|
1135 |
|
|
* libmdtools/: SimInfo.cpp, SimInfo.hpp, fSimulation.h, |
1136 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: working on adding |
1137 |
|
|
the box matrix to everything. |
1138 |
|
|
|
1139 |
tim |
837 |
2003-06-30 18:03 mmeineke |
1140 |
tim |
660 |
|
1141 |
|
|
* ChangeLog, libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
1142 |
|
|
src/oopse.cpp: |
1143 |
|
|
Updated the ChangeLog, and Converted most of the SImInfo to use |
1144 |
|
|
non-Isotropic boxes. wrapVector needs to be finished. |
1145 |
|
|
|
1146 |
tim |
837 |
2003-06-25 17:12 mmeineke |
1147 |
mmeineke |
568 |
|
1148 |
|
|
* libmdtools/: Integrator.cpp, SimSetup.cpp: Changed over the bonds |
1149 |
|
|
to Harmonic bonds in the DUFF frc file |
1150 |
|
|
|
1151 |
|
|
fixed constraints. |
1152 |
|
|
|
1153 |
tim |
837 |
2003-06-25 17:11 mmeineke |
1154 |
mmeineke |
568 |
|
1155 |
|
|
* forceFields/DUFF.frc: Changed over the bonds to Harmonic bonds in |
1156 |
|
|
the DUFF frc file |
1157 |
|
|
|
1158 |
tim |
837 |
2003-06-24 18:51 gezelter |
1159 |
mmeineke |
568 |
|
1160 |
|
|
* libmdtools/: Integrator.hpp, NVT.cpp: Fixes to NVT. Check them! |
1161 |
|
|
|
1162 |
tim |
837 |
2003-06-24 15:57 mmeineke |
1163 |
mmeineke |
568 |
|
1164 |
|
|
* forceFields/DUFF.frc, libmdtools/BondExtensions.cpp, |
1165 |
|
|
libmdtools/DUFF.cpp, libmdtools/SRI.hpp: added Harmonic bod into |
1166 |
|
|
the DUFF forcefield and BondExtensions.cpp |
1167 |
|
|
|
1168 |
tim |
837 |
2003-06-23 17:24 mmeineke |
1169 |
mmeineke |
568 |
|
1170 |
|
|
* libmdtools/Integrator.cpp: Doing some work to debug the |
1171 |
|
|
constraint code. |
1172 |
|
|
|
1173 |
tim |
837 |
2003-06-20 16:50 gezelter |
1174 |
mmeineke |
568 |
|
1175 |
|
|
* libmdtools/Integrator.hpp: NPT fix |
1176 |
|
|
|
1177 |
tim |
837 |
2003-06-20 16:29 mmeineke |
1178 |
mmeineke |
568 |
|
1179 |
|
|
* libmdtools/Atom.cpp, libmdtools/DUFF.cpp, |
1180 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Integrator.cpp, |
1181 |
|
|
libmdtools/Integrator.hpp, libmdtools/LJFF.cpp, |
1182 |
|
|
libmdtools/Makefile, libmdtools/NVT.cpp, libmdtools/SimSetup.cpp, |
1183 |
|
|
libmdtools/Thermo.hpp, src/Makefile, utils/Makefile: Most of the |
1184 |
|
|
integrator and NVT seem to be working now. |
1185 |
|
|
|
1186 |
tim |
837 |
2003-06-20 12:49 gezelter |
1187 |
mmeineke |
568 |
|
1188 |
|
|
* libmdtools/: Integrator.hpp, NVT.cpp: NVT additions |
1189 |
|
|
|
1190 |
tim |
837 |
2003-06-19 18:02 mmeineke |
1191 |
mmeineke |
568 |
|
1192 |
|
|
* forceFields/DUFF.frc, forceFields/LJFF.frc, |
1193 |
|
|
forceFields/LJ_FF.frc, forceFields/Makefile, |
1194 |
|
|
forceFields/TraPPE.frc, forceFields/TraPPE_Ex.frc, |
1195 |
|
|
libmdtools/DUFF.cpp, libmdtools/ForceFields.hpp, |
1196 |
|
|
libmdtools/Integrator.cpp, libmdtools/Integrator.hpp, |
1197 |
|
|
libmdtools/LJFF.cpp, libmdtools/LJ_FF.cpp, libmdtools/Makefile, |
1198 |
|
|
libmdtools/TraPPEFF.cpp: slowly converting to new integrator and |
1199 |
|
|
forcefield names. |
1200 |
|
|
|
1201 |
tim |
837 |
2003-06-19 15:21 mmeineke |
1202 |
mmeineke |
568 |
|
1203 |
|
|
* libmdtools/: Integrator.cpp, SimSetup.cpp, Symplectic.cpp: |
1204 |
|
|
finished the basics of the integrator and SimSetup.cpp |
1205 |
|
|
|
1206 |
tim |
837 |
2003-06-19 15:11 mmeineke |
1207 |
mmeineke |
568 |
|
1208 |
|
|
* libmdtools/SimSetup.cpp: doing some work on SimSetup to clean it |
1209 |
|
|
up / get it to work with the new Integrator. |
1210 |
|
|
|
1211 |
tim |
837 |
2003-06-18 18:20 mmeineke |
1212 |
mmeineke |
568 |
|
1213 |
|
|
* libmdtools/Symplectic.cpp: minor changes in an attempt to fix |
1214 |
|
|
output times. |
1215 |
|
|
|
1216 |
tim |
837 |
2003-06-17 17:56 mmeineke |
1217 |
mmeineke |
568 |
|
1218 |
|
|
* libmdtools/: Integrator.hpp, SimSetup.cpp: Added Teng's parmeters |
1219 |
|
|
fro the ghost Bend in TraPPE_Ex |
1220 |
|
|
|
1221 |
|
|
some work on the integrator. ( incomplete) |
1222 |
|
|
|
1223 |
tim |
837 |
2003-06-17 17:55 mmeineke |
1224 |
mmeineke |
568 |
|
1225 |
|
|
* forceFields/TraPPE_Ex.frc: Added Teng's parmeters fro the ghost |
1226 |
|
|
Bend in TraPPE_Ex |
1227 |
|
|
|
1228 |
tim |
837 |
2003-06-04 17:06 mmeineke |
1229 |
mmeineke |
568 |
|
1230 |
|
|
* libmdtools/: Integrator.hpp, Symplectic.cpp: added constrainA and |
1231 |
|
|
constrainB to the Symplectic integrator |
1232 |
|
|
|
1233 |
tim |
837 |
2003-05-30 17:32 mmeineke |
1234 |
mmeineke |
568 |
|
1235 |
|
|
* utils/bilayerSys.cpp: currently modifiying Symplectic to become |
1236 |
|
|
the basic integrator. |
1237 |
|
|
|
1238 |
|
|
bilayerSys.cpp altered for building tb3. |
1239 |
|
|
|
1240 |
tim |
837 |
2003-05-30 17:31 mmeineke |
1241 |
mmeineke |
568 |
|
1242 |
|
|
* libmdtools/: Integrator.hpp, SimInfo.hpp, Symplectic.cpp, |
1243 |
|
|
TraPPE_ExFF.cpp, Verlet.cpp, f_verlet_constrained.F90: currently |
1244 |
|
|
modifiying Symplectic to become the basic integrator. |
1245 |
|
|
|
1246 |
tim |
837 |
2003-05-30 16:19 mmeineke |
1247 |
mmeineke |
568 |
|
1248 |
|
|
* libmdtools/Integrator.hpp: added some member variables for |
1249 |
|
|
position, velocity, etc. |
1250 |
|
|
|
1251 |
tim |
837 |
2003-05-30 15:07 mmeineke |
1252 |
mmeineke |
568 |
|
1253 |
|
|
* libmdtools/: AbstractClasses.hpp, Integrator.hpp: changed how NVT |
1254 |
|
|
is now derived from Integrator |
1255 |
|
|
|
1256 |
tim |
837 |
2003-05-20 12:44 mmeineke |
1257 |
mmeineke |
568 |
|
1258 |
|
|
* libmdtools/GhostBend.cpp: fixed an a mismatched Ghostbend bug. |
1259 |
|
|
|
1260 |
tim |
837 |
2003-05-17 12:57 mmeineke |
1261 |
mmeineke |
568 |
|
1262 |
|
|
* utils/: Makefile, MoLocator.cpp, bilayerSys.cpp: all seems to be |
1263 |
|
|
working |
1264 |
|
|
|
1265 |
tim |
837 |
2003-05-16 17:37 mmeineke |
1266 |
mmeineke |
568 |
|
1267 |
|
|
* utils/bilayerSys.cpp: still working on the bilayer code |
1268 |
|
|
|
1269 |
tim |
837 |
2003-05-16 10:28 mmeineke |
1270 |
mmeineke |
568 |
|
1271 |
|
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: doing some |
1272 |
|
|
work to overhaul sysbuild. |
1273 |
|
|
|
1274 |
tim |
837 |
2003-05-13 17:23 mmeineke |
1275 |
mmeineke |
568 |
|
1276 |
|
|
* libmdtools/calc_sticky_pair.F90: optimized the ssd calc loop |
1277 |
|
|
|
1278 |
tim |
837 |
2003-05-13 16:47 mmeineke |
1279 |
mmeineke |
568 |
|
1280 |
|
|
* samples/: Makefile, beadLipid/Makefile, beadLipid/beadLipid.mdl, |
1281 |
|
|
beadLipid/water.mdl: Added bead lipid model to the sample directory |
1282 |
|
|
|
1283 |
tim |
837 |
2003-05-13 16:34 mmeineke |
1284 |
mmeineke |
568 |
|
1285 |
|
|
* forceFields/TraPPE_Ex.frc: finished adding the Tail beads into |
1286 |
|
|
the Trappe extended force field |
1287 |
|
|
|
1288 |
tim |
837 |
2003-05-13 13:01 mmeineke |
1289 |
mmeineke |
568 |
|
1290 |
|
|
* forceFields/TraPPE_Ex.frc: added the TailBead atom types to the |
1291 |
|
|
TraPPe_Ex forceField |
1292 |
|
|
|
1293 |
tim |
837 |
2003-05-09 15:51 mmeineke |
1294 |
mmeineke |
568 |
|
1295 |
|
|
* samples/lipid/lipid.mdl: fixed up the TraPPE_Ex force field. |
1296 |
|
|
there were some duplicate entries |
1297 |
|
|
|
1298 |
|
|
added a two chain lipid to the lipid.mdl in sample |
1299 |
|
|
|
1300 |
tim |
837 |
2003-05-09 15:51 mmeineke |
1301 |
mmeineke |
568 |
|
1302 |
|
|
* forceFields/TraPPE_Ex.frc: fixed up the TraPPE_Ex force field. |
1303 |
|
|
there were some duplicate entries |
1304 |
|
|
|
1305 |
tim |
837 |
2003-05-09 12:56 mmeineke |
1306 |
mmeineke |
568 |
|
1307 |
|
|
* forceFields/TraPPE_Ex.frc: added the utils subdirectory to the |
1308 |
|
|
configure script |
1309 |
|
|
|
1310 |
|
|
added the CH branching group to the TraPPE_Ex fource field |
1311 |
|
|
|
1312 |
tim |
837 |
2003-05-09 12:55 mmeineke |
1313 |
mmeineke |
568 |
|
1314 |
|
|
* ac-tools/configure.in: added the utils subdirectory to the |
1315 |
|
|
configure script |
1316 |
|
|
|
1317 |
tim |
837 |
2003-04-25 12:02 mmeineke |
1318 |
mmeineke |
568 |
|
1319 |
|
|
* utils/bilayerSys.cpp: i quick fix to th distance in the random |
1320 |
|
|
bilayer builder |
1321 |
|
|
|
1322 |
tim |
837 |
2003-04-24 22:00 mmeineke |
1323 |
mmeineke |
568 |
|
1324 |
|
|
* libmdtools/f_verlet_constrained.F90: added a new test for |
1325 |
|
|
constraint failure |
1326 |
|
|
|
1327 |
tim |
837 |
2003-04-17 17:54 mmeineke |
1328 |
mmeineke |
568 |
|
1329 |
|
|
* libBASS/BASS_interface.h, libmdtools/SimSetup.cpp, |
1330 |
|
|
utils/Makefile, utils/MoLocator.cpp, utils/MoLocator.hpp, |
1331 |
|
|
utils/bilayerSys.cpp: fixed up sysBuild to where it should now |
1332 |
|
|
build our systems |
1333 |
|
|
|
1334 |
tim |
837 |
2003-04-16 17:11 mmeineke |
1335 |
mmeineke |
568 |
|
1336 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp: almost finished. |
1337 |
|
|
|
1338 |
tim |
837 |
2003-04-15 17:47 mmeineke |
1339 |
mmeineke |
568 |
|
1340 |
|
|
* utils/: bilayerSys.cpp, sysBuild.cpp, sysBuild.hpp: bilayerSys |
1341 |
|
|
and sysBuild both will build now. woot! |
1342 |
|
|
|
1343 |
tim |
837 |
2003-04-15 17:20 mmeineke |
1344 |
mmeineke |
568 |
|
1345 |
|
|
* utils/: MoLocator.cpp, MoLocator.hpp, bilayerSys.cpp, |
1346 |
|
|
bilayerSys.hpp, sysBuild.cpp, sysBuild.hpp: finished bilayerSys.cpp |
1347 |
|
|
|
1348 |
|
|
sysBuild still need to write the bass file. |
1349 |
|
|
|
1350 |
|
|
MoLocator.cpp is currently empty |
1351 |
|
|
|
1352 |
tim |
837 |
2003-04-15 16:40 chuckv |
1353 |
mmeineke |
568 |
|
1354 |
|
|
* forceFields/EAM_FF.frc, forceFields/agu3.eam, |
1355 |
|
|
forceFields/auu3.eam, forceFields/cuu3.eam, forceFields/niu3.eam, |
1356 |
|
|
forceFields/pdu3.eam, forceFields/ptu3.eam, |
1357 |
|
|
libmdtools/ForceFields.hpp: Added eam force files... |
1358 |
|
|
|
1359 |
tim |
837 |
2003-04-15 12:37 chuckv |
1360 |
mmeineke |
568 |
|
1361 |
|
|
* libmdtools/EAM_FF.cpp: More eam work. |
1362 |
|
|
|
1363 |
tim |
837 |
2003-04-14 17:22 mmeineke |
1364 |
mmeineke |
568 |
|
1365 |
|
|
* libmdtools/SimSetup.hpp, utils/Makefile, utils/bilayerSys.cpp, |
1366 |
|
|
utils/bilayerSys.hpp, utils/sysBuild.cpp, utils/sysBuild.hpp: |
1367 |
|
|
working on the system builder |
1368 |
|
|
|
1369 |
tim |
837 |
2003-04-14 17:16 chuckv |
1370 |
mmeineke |
568 |
|
1371 |
|
|
* libmdtools/: Symplectic.cpp, Verlet.cpp, calc_eam.F90: Fixed |
1372 |
|
|
ordering on NVT calculation in integrators. |
1373 |
|
|
|
1374 |
tim |
837 |
2003-04-14 15:51 mmeineke |
1375 |
mmeineke |
568 |
|
1376 |
|
|
* utils/: Makefile, sysBuild.cpp, MPIobj/placeHolder, |
1377 |
|
|
obj/placeHolder: working on a system builder |
1378 |
|
|
|
1379 |
tim |
837 |
2003-04-14 15:04 mmeineke |
1380 |
mmeineke |
568 |
|
1381 |
|
|
* utils/Makefile: added Ghost bends to the TraPPE_Ex forceField |
1382 |
|
|
|
1383 |
|
|
added sysBuild to the utils Makefile |
1384 |
|
|
|
1385 |
tim |
837 |
2003-04-14 15:03 mmeineke |
1386 |
mmeineke |
568 |
|
1387 |
|
|
* forceFields/TraPPE_Ex.frc, libmdtools/TraPPE_ExFF.cpp: added |
1388 |
|
|
Ghost bends to the TraPPE_Ex forceField |
1389 |
|
|
|
1390 |
tim |
837 |
2003-04-14 14:19 chuckv |
1391 |
mmeineke |
568 |
|
1392 |
|
|
* libmdtools/calc_eam.F90: Added first mangling of EAM. |
1393 |
|
|
|
1394 |
tim |
837 |
2003-04-11 14:46 mmeineke |
1395 |
mmeineke |
568 |
|
1396 |
|
|
* libmdtools/: SimSetup.cpp, calc_LJ_FF.F90, force_globals.F90, |
1397 |
|
|
simulation_module.F90: fixed a memory bug in Fortran, where |
1398 |
|
|
molMembershipArray was declared nLocal instead of nGlobal. |
1399 |
|
|
|
1400 |
tim |
837 |
2003-04-11 11:16 gezelter |
1401 |
mmeineke |
568 |
|
1402 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
1403 |
|
|
SimSetup.cpp, calc_LJ_FF.F90, do_Forces.F90, |
1404 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: Bug fix in progress |
1405 |
|
|
for NPT |
1406 |
|
|
|
1407 |
tim |
837 |
2003-04-10 16:08 mmeineke |
1408 |
mmeineke |
568 |
|
1409 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp, SimSetup.cpp: added a |
1410 |
|
|
globalIndex counter to Molecule |
1411 |
|
|
|
1412 |
tim |
837 |
2003-04-10 12:35 gezelter |
1413 |
mmeineke |
568 |
|
1414 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp: Working on |
1415 |
|
|
ConstantStress |
1416 |
|
|
|
1417 |
tim |
837 |
2003-04-10 12:27 mmeineke |
1418 |
mmeineke |
568 |
|
1419 |
|
|
* libmdtools/SimSetup.cpp: fixed a n mpi init bug in SimSetup. |
1420 |
|
|
caused a miscalculation of nLocal. |
1421 |
|
|
|
1422 |
tim |
837 |
2003-04-10 12:21 mmeineke |
1423 |
mmeineke |
568 |
|
1424 |
|
|
* libmdtools/: Symplectic.cpp, Thermo.cpp, calc_dipole_dipole.F90, |
1425 |
|
|
do_Forces.F90: fixed a bug in symplectic, where presure was only |
1426 |
|
|
being calculated the first time through. |
1427 |
|
|
|
1428 |
tim |
837 |
2003-04-09 12:20 chuckv |
1429 |
mmeineke |
568 |
|
1430 |
|
|
* samples/alkane/alkanes.mdl: added pentane to the alkane model |
1431 |
|
|
file |
1432 |
|
|
|
1433 |
tim |
837 |
2003-04-09 09:59 gezelter |
1434 |
mmeineke |
568 |
|
1435 |
|
|
* libmdtools/: ExtendedSystem.cpp, ForceFields.cpp, StatWriter.cpp, |
1436 |
|
|
Thermo.cpp, Thermo.hpp: Added volume and enthalpy to status file |
1437 |
|
|
|
1438 |
tim |
837 |
2003-04-09 00:06 gezelter |
1439 |
mmeineke |
568 |
|
1440 |
|
|
* libmdtools/: DumpWriter.cpp, ExtendedSystem.cpp, |
1441 |
|
|
ExtendedSystem.hpp, Molecule.cpp, Molecule.hpp, SimInfo.cpp, |
1442 |
|
|
SimInfo.hpp, SimSetup.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, |
1443 |
|
|
Verlet.cpp, calc_LJ_FF.F90, calc_dipole_dipole.F90, calc_gb.F90, |
1444 |
|
|
calc_reaction_field.F90, calc_sticky_pair.F90, |
1445 |
|
|
fortranWrapDefines.hpp, simulation_module.F90: fixes for NPT and |
1446 |
|
|
NVT |
1447 |
|
|
|
1448 |
tim |
837 |
2003-04-08 18:38 chuckv |
1449 |
mmeineke |
568 |
|
1450 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/Symplectic.cpp, |
1451 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
1452 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
1453 |
|
|
libmdtools/simulation_module.F90, samples/water/ssd.bass: It works |
1454 |
|
|
(kinda)... |
1455 |
|
|
|
1456 |
tim |
837 |
2003-04-08 17:35 gezelter |
1457 |
mmeineke |
568 |
|
1458 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1459 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/ExtendedSystem.hpp, |
1460 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT / NVT |
1461 |
|
|
|
1462 |
tim |
837 |
2003-04-08 13:16 chuckv |
1463 |
mmeineke |
568 |
|
1464 |
|
|
* libmdtools/: do_Forces.F90, neighborLists.F90, |
1465 |
|
|
simulation_module.F90: Moved expand neighborlist to init_FF. |
1466 |
|
|
|
1467 |
tim |
837 |
2003-04-08 11:20 chuckv |
1468 |
mmeineke |
568 |
|
1469 |
|
|
* libmdtools/: ForceFields.cpp, Thermo.cpp, Verlet.cpp: fixes for |
1470 |
|
|
NVT |
1471 |
|
|
|
1472 |
tim |
837 |
2003-04-08 10:39 gezelter |
1473 |
mmeineke |
568 |
|
1474 |
|
|
* libmdtools/Verlet.cpp: fixes for nvt / npt |
1475 |
|
|
|
1476 |
tim |
837 |
2003-04-08 10:34 gezelter |
1477 |
mmeineke |
568 |
|
1478 |
|
|
* libmdtools/: ExtendedSystem.cpp, StatWriter.cpp, Symplectic.cpp, |
1479 |
|
|
Thermo.cpp, Verlet.cpp: dt/2 fix in nvt |
1480 |
|
|
|
1481 |
tim |
837 |
2003-04-08 08:50 gezelter |
1482 |
mmeineke |
568 |
|
1483 |
|
|
* libmdtools/ExtendedSystem.cpp: Fixes for affine transform |
1484 |
|
|
|
1485 |
tim |
837 |
2003-04-08 08:44 gezelter |
1486 |
mmeineke |
568 |
|
1487 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
1488 |
|
|
Symplectic.cpp, Thermo.cpp, Verlet.cpp: Changes to integrate the |
1489 |
|
|
NVT and NPT ensembles |
1490 |
|
|
|
1491 |
tim |
837 |
2003-04-07 17:42 gezelter |
1492 |
mmeineke |
568 |
|
1493 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, |
1494 |
|
|
libmdtools/ExtendedSystem.cpp, libmdtools/SimInfo.cpp, |
1495 |
|
|
libmdtools/SimSetup.cpp: Fixes for NPT and NVT |
1496 |
|
|
|
1497 |
tim |
837 |
2003-04-07 17:20 mmeineke |
1498 |
mmeineke |
568 |
|
1499 |
|
|
* libmdtools/calc_sticky_pair.F90: fixed a sign error in the radial |
1500 |
|
|
portion of SSD. |
1501 |
|
|
|
1502 |
tim |
837 |
2003-04-07 17:16 mmeineke |
1503 |
mmeineke |
568 |
|
1504 |
|
|
* libmdtools/: ForceFields.cpp, Symplectic.cpp: |
1505 |
|
|
doing some testing in sticky through Symplectic. |
1506 |
|
|
|
1507 |
tim |
837 |
2003-04-07 16:51 gezelter |
1508 |
mmeineke |
568 |
|
1509 |
|
|
* libmdtools/: ExtendedSystem.cpp, Verlet.cpp: Working on NVT |
1510 |
|
|
|
1511 |
tim |
837 |
2003-04-07 16:50 chuckv |
1512 |
mmeineke |
568 |
|
1513 |
|
|
* libmdtools/do_Forces.F90: Fixed transpose bug in mpi reduce for |
1514 |
|
|
tau and virial. |
1515 |
|
|
|
1516 |
tim |
837 |
2003-04-07 16:06 mmeineke |
1517 |
mmeineke |
568 |
|
1518 |
|
|
* libmdtools/DumpWriter.cpp, libmdtools/SimInfo.cpp, |
1519 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Symplectic.cpp, |
1520 |
|
|
libmdtools/calc_dipole_dipole.F90, libmdtools/calc_sticky_pair.F90, |
1521 |
|
|
src/Makefile: bug fixes |
1522 |
|
|
|
1523 |
tim |
837 |
2003-04-07 12:56 gezelter |
1524 |
mmeineke |
568 |
|
1525 |
|
|
* libmdtools/: ExtendedSystem.cpp, Molecule.cpp, Molecule.hpp, |
1526 |
|
|
StatWriter.cpp, Symplectic.cpp, Thermo.cpp, Thermo.hpp, Verlet.cpp: |
1527 |
|
|
Many fixes to add extended system |
1528 |
|
|
|
1529 |
tim |
837 |
2003-04-07 10:30 gezelter |
1530 |
mmeineke |
568 |
|
1531 |
|
|
* src/Makefile: Fixed a bug caused by my experimentation |
1532 |
|
|
|
1533 |
tim |
837 |
2003-04-07 10:30 gezelter |
1534 |
mmeineke |
568 |
|
1535 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, |
1536 |
|
|
Integrator.hpp, Makefile, SimSetup.cpp, Symplectic.cpp, Verlet.cpp: |
1537 |
|
|
Added ExtendedSystem infrastructure for NPT and NVT calculations |
1538 |
|
|
|
1539 |
tim |
837 |
2003-04-07 10:30 gezelter |
1540 |
mmeineke |
568 |
|
1541 |
|
|
* libBASS/: Globals.cpp, Globals.hpp: Added targetPressure to BASS |
1542 |
|
|
|
1543 |
|
|
2003-04-04 23:07 gezelter |
1544 |
|
|
|
1545 |
|
|
* src/Makefile: final mods to try a fortran compiler |
1546 |
|
|
|
1547 |
|
|
2003-04-04 22:39 gezelter |
1548 |
|
|
|
1549 |
|
|
* libmdtools/: LJ_FF.cpp, SimInfo.cpp, TraPPE_ExFF.cpp, |
1550 |
|
|
fortranWrapDefines.hpp: Bug fixes for simulation module rewrites |
1551 |
|
|
|
1552 |
|
|
2003-04-04 21:56 gezelter |
1553 |
|
|
|
1554 |
|
|
* libmdtools/: Makefile, atype_module.F90, do_Forces.F90, |
1555 |
|
|
fortranWrappers.cpp, wrappers.F90: bug fixes for compilation |
1556 |
|
|
|
1557 |
|
|
2003-04-04 21:45 gezelter |
1558 |
|
|
|
1559 |
|
|
* libmdtools/: fortranWrapDefines.hpp, fortranWrappers.hpp: bug |
1560 |
|
|
fixes to fortran wrappers |
1561 |
|
|
|
1562 |
|
|
2003-04-04 17:22 chuckv |
1563 |
|
|
|
1564 |
|
|
* libmdtools/: Makefile, calc_LJ_FF.F90, calc_dipole_dipole.F90, |
1565 |
|
|
calc_gb.F90, calc_reaction_field.F90, calc_sticky_pair.F90, |
1566 |
|
|
do_Forces.F90, fortranWrapDefines.hpp, fortranWrappers.cpp, |
1567 |
|
|
simulation_module.F90, wrappers.F90: Breaking c and fortran, c gets |
1568 |
|
|
smarter, fortran gets dumber... |
1569 |
|
|
|
1570 |
|
|
2003-04-04 14:57 mmeineke |
1571 |
|
|
|
1572 |
|
|
* libmdtools/: calc_dipole_dipole.F90, do_Forces.F90, |
1573 |
|
|
neighborLists.F90: fixed a memory read bug in neighborlist |
1574 |
|
|
|
1575 |
|
|
2003-04-04 14:47 gezelter |
1576 |
|
|
|
1577 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
1578 |
|
|
SimInfo.hpp, Thermo.cpp: Changes for Extended System |
1579 |
|
|
|
1580 |
|
|
2003-04-04 14:16 gezelter |
1581 |
|
|
|
1582 |
|
|
* libmdtools/: ExtendedSystem.cpp, ExtendedSystem.hpp, SimInfo.cpp, |
1583 |
|
|
SimInfo.hpp: Fixes for ExtendedSystem |
1584 |
|
|
|
1585 |
|
|
2003-04-03 20:57 gezelter |
1586 |
|
|
|
1587 |
|
|
* libmdtools/ExtendedSystem.hpp: Added extended system header |
1588 |
|
|
|
1589 |
|
|
2003-04-03 20:57 gezelter |
1590 |
|
|
|
1591 |
|
|
* libmdtools/: ExtendedSystem.cpp, Thermo.cpp, Thermo.hpp: changes |
1592 |
|
|
for extended system code |
1593 |
|
|
|
1594 |
|
|
2003-04-03 18:49 gezelter |
1595 |
|
|
|
1596 |
|
|
* libmdtools/: ExtendedSystem.cpp, NVT.cpp: renamed nvt to |
1597 |
|
|
extendedsystem |
1598 |
|
|
|
1599 |
|
|
2003-04-03 17:19 mmeineke |
1600 |
|
|
|
1601 |
|
|
* libmdtools/Molecule.hpp: added some little fixes here and there. |
1602 |
|
|
|
1603 |
|
|
2003-04-03 17:01 mmeineke |
1604 |
|
|
|
1605 |
|
|
* libmdtools/TraPPE_ExFF.cpp: fixed a possible call before |
1606 |
|
|
initialize bug. |
1607 |
|
|
|
1608 |
|
|
2003-04-03 16:12 mmeineke |
1609 |
|
|
|
1610 |
|
|
* libmdtools/: DumpWriter.cpp, Molecule.cpp, randomSPRNG.hpp: just |
1611 |
|
|
little things like deleteing unused variables and such. |
1612 |
|
|
|
1613 |
|
|
2003-04-03 15:57 mmeineke |
1614 |
|
|
|
1615 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: a few fixes to |
1616 |
|
|
simError.h also some fixes to Molecule.hpp |
1617 |
|
|
|
1618 |
|
|
2003-04-03 15:57 mmeineke |
1619 |
|
|
|
1620 |
|
|
* libBASS/simError.h: a few fixes to simError.h |
1621 |
|
|
|
1622 |
|
|
2003-04-03 15:21 mmeineke |
1623 |
|
|
|
1624 |
|
|
* libBASS/Makefile, libBASS/mpiBASS.c, libBASS/simError.c, |
1625 |
|
|
libBASS/simError.h, libmdtools/DumpWriter.cpp, |
1626 |
|
|
libmdtools/ForceFields.cpp, libmdtools/InitializeFromFile.cpp, |
1627 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Makefile, libmdtools/Thermo.cpp, |
1628 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp, |
1629 |
|
|
src/Makefile, src/oopse.cpp: fixed some small things with |
1630 |
|
|
simError.h |
1631 |
|
|
|
1632 |
|
|
2003-04-03 15:19 gezelter |
1633 |
|
|
|
1634 |
|
|
* libmdtools/: Molecule.cpp, Molecule.hpp: Starting work on NPT |
1635 |
|
|
|
1636 |
|
|
2003-04-03 14:58 gezelter |
1637 |
|
|
|
1638 |
|
|
* libmdtools/: NVT.cpp, Thermo.cpp: Added NVT file (very broken for |
1639 |
|
|
now) |
1640 |
|
|
|
1641 |
|
|
2003-04-03 08:42 gezelter |
1642 |
|
|
|
1643 |
|
|
* README, libmdtools/Thermo.cpp, utils/Makefile, utils/quickLate.c: |
1644 |
|
|
Changed Readme, added some files |
1645 |
|
|
|
1646 |
|
|
2003-04-02 17:19 mmeineke |
1647 |
|
|
|
1648 |
|
|
* libmdtools/: ForceFields.cpp, SimInfo.cpp, SimSetup.cpp, |
1649 |
|
|
Symplectic.cpp, calc_dipole_dipole.F90, calc_sticky_pair.F90: |
1650 |
|
|
dipoles mostly work, but there is a memory leak somewhere. |
1651 |
|
|
|
1652 |
|
|
2003-04-02 10:01 mmeineke |
1653 |
|
|
|
1654 |
|
|
* libmdtools/TraPPE_ExFF.cpp: Fixed a bug where MPI was not getting |
1655 |
|
|
the proper atomIdents. |
1656 |
|
|
|
1657 |
|
|
2003-04-01 11:50 chuckv |
1658 |
|
|
|
1659 |
|
|
* libmdtools/SimInfo.cpp, libmdtools/do_Forces.F90, |
1660 |
|
|
libmdtools/mpiSimulation.cpp, libmdtools/mpiSimulation_module.F90, |
1661 |
|
|
samples/argon/argon.bass: more bug fixes.... |
1662 |
|
|
|
1663 |
|
|
2003-04-01 11:49 mmeineke |
1664 |
|
|
|
1665 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixed |
1666 |
|
|
DumpWriter to be more robust to errors. also added a little |
1667 |
|
|
namespace to InitFromFile to wrap it's helper functions in MPI |
1668 |
|
|
|
1669 |
|
|
2003-03-31 17:09 chuckv |
1670 |
|
|
|
1671 |
|
|
* libmdtools/: SimInfo.cpp, do_Forces.F90: Fixed bug with pot_local |
1672 |
|
|
not zeroed. |
1673 |
|
|
|
1674 |
|
|
2003-03-31 16:50 chuckv |
1675 |
|
|
|
1676 |
|
|
* libmdtools/BendExtensions.cpp, libmdtools/Exclude.cpp, |
1677 |
|
|
libmdtools/ForceFields.cpp, libmdtools/Molecule.cpp, |
1678 |
|
|
libmdtools/Molecule.hpp, libmdtools/SimInfo.cpp, |
1679 |
|
|
libmdtools/SimSetup.cpp, libmdtools/Thermo.cpp, |
1680 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/do_Forces.F90, |
1681 |
|
|
samples/alkane/butane.bass: Fixes in MPI force calc and in |
1682 |
|
|
Trappe_Ex parsing. |
1683 |
|
|
|
1684 |
|
|
2003-03-28 17:34 chuckv |
1685 |
|
|
|
1686 |
|
|
* libmdtools/DumpWriter.cpp: bug fix in DumpWriter.cpp |
1687 |
|
|
|
1688 |
|
|
2003-03-28 16:45 chuckv |
1689 |
|
|
|
1690 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
1691 |
|
|
libmdtools/InitializeFromFile.cpp: Bug fixes in read-write |
1692 |
|
|
routines. |
1693 |
|
|
|
1694 |
|
|
2003-03-28 14:33 mmeineke |
1695 |
|
|
|
1696 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.cpp, |
1697 |
|
|
Molecule.hpp, SRI.hpp, SimSetup.cpp, simulation_module.F90: fixed a |
1698 |
|
|
bug where the Excludes were not being created properly |
1699 |
|
|
|
1700 |
|
|
2003-03-28 14:30 chuckv |
1701 |
|
|
|
1702 |
|
|
* libBASS/Makefile, libmdtools/DumpWriter.cpp, |
1703 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/SimSetup.cpp, |
1704 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/mpiSimulation.cpp: mpi fixes |
1705 |
|
|
and debugging mpi read write from file. |
1706 |
|
|
|
1707 |
|
|
2003-03-28 10:28 mmeineke |
1708 |
|
|
|
1709 |
|
|
* libmdtools/: LJ_FF.cpp, TraPPE_ExFF.cpp: fixed long range |
1710 |
|
|
interactions in Trappe |
1711 |
|
|
|
1712 |
|
|
2003-03-27 18:33 chuckv |
1713 |
|
|
|
1714 |
|
|
* libmdtools/: SimSetup.cpp, mpiSimulation.cpp, |
1715 |
|
|
mpiSimulation_module.F90: MPI buggy, fixed mpiRefresh issue. |
1716 |
|
|
|
1717 |
|
|
2003-03-27 17:16 mmeineke |
1718 |
|
|
|
1719 |
|
|
* libmdtools/: Exclude.cpp, SimSetup.cpp: fixed a bug where |
1720 |
|
|
excludes were not being initialized |
1721 |
|
|
|
1722 |
|
|
2003-03-27 16:52 mmeineke |
1723 |
|
|
|
1724 |
|
|
* src/Makefile: [no log message] |
1725 |
|
|
|
1726 |
|
|
2003-03-27 16:52 mmeineke |
1727 |
|
|
|
1728 |
|
|
* libmdtools/SimSetup.cpp: Fixed a single processor segfault bug. |
1729 |
|
|
|
1730 |
|
|
2003-03-27 16:07 mmeineke |
1731 |
|
|
|
1732 |
|
|
* libmdtools/: Exclude.cpp, ForceFields.cpp, LJ_FF.cpp, |
1733 |
|
|
Molecule.cpp, Symplectic.cpp, Thermo.cpp, TraPPE_ExFF.cpp, |
1734 |
|
|
Verlet.cpp: fixed the compile time bugs, Source builds and links |
1735 |
|
|
|
1736 |
|
|
2003-03-27 15:48 mmeineke |
1737 |
|
|
|
1738 |
|
|
* libmdtools/: Molecule.cpp, SimInfo.hpp, SimSetup.cpp: fixed a few |
1739 |
|
|
more bugs. |
1740 |
|
|
|
1741 |
|
|
2003-03-27 15:40 mmeineke |
1742 |
|
|
|
1743 |
|
|
* libmdtools/Molecule.cpp: added the Molecule.cpp file |
1744 |
|
|
|
1745 |
|
|
2003-03-27 15:39 mmeineke |
1746 |
|
|
|
1747 |
|
|
* libmdtools/: Makefile, Molecule.hpp: fixed the makefile |
1748 |
|
|
|
1749 |
|
|
2003-03-27 15:36 mmeineke |
1750 |
|
|
|
1751 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
1752 |
|
|
ForceFields.hpp, LJ_FF.cpp, Makefile, Molecule.hpp, SimInfo.cpp, |
1753 |
|
|
SimSetup.cpp, SimSetup.hpp: fixing some compile time bugs |
1754 |
|
|
|
1755 |
|
|
2003-03-27 15:12 mmeineke |
1756 |
|
|
|
1757 |
|
|
* libmdtools/: AbstractClasses.hpp, ForceFields.cpp, |
1758 |
|
|
Integrator.hpp, Molecule.hpp, Symplectic.cpp, Thermo.cpp, |
1759 |
|
|
Verlet.cpp: I have implemeted Molecules everywhere I could remember |
1760 |
|
|
to. will now attempt to compile. |
1761 |
|
|
|
1762 |
|
|
2003-03-27 14:21 mmeineke |
1763 |
|
|
|
1764 |
|
|
* libmdtools/: Molecule.hpp, SimInfo.hpp, SimSetup.cpp, |
1765 |
|
|
SimSetup.hpp, mpiSimulation.cpp, mpiSimulation.hpp: finished |
1766 |
|
|
updating SimSetup to initialize and use the new MPI division of |
1767 |
|
|
labour, and Molecule class |
1768 |
|
|
|
1769 |
|
|
2003-03-27 12:55 mmeineke |
1770 |
|
|
|
1771 |
|
|
* libmdtools/TraPPE_ExFF.cpp: finished conversion of TraPPE_ExFF to |
1772 |
|
|
use Molecule |
1773 |
|
|
|
1774 |
|
|
2003-03-27 12:32 mmeineke |
1775 |
|
|
|
1776 |
|
|
* libmdtools/: ForceFields.cpp, ForceFields.hpp, LJ_FF.cpp, |
1777 |
|
|
SimInfo.cpp, SimSetup.cpp, TraPPE_ExFF.cpp: LJ_FF has been |
1778 |
|
|
converted to the new Molecule model. TraPPE_Ex is currently being |
1779 |
|
|
updated. SimSetups routines are writtten, but not yet called. |
1780 |
|
|
|
1781 |
|
|
2003-03-27 10:07 gezelter |
1782 |
|
|
|
1783 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp, |
1784 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp: fixes for local->global atom |
1785 |
|
|
numbering in MPI |
1786 |
|
|
|
1787 |
|
|
2003-03-27 09:30 mmeineke |
1788 |
|
|
|
1789 |
|
|
* libmdtools/mpiSimulation.cpp: little bug fixes here and there. |
1790 |
|
|
|
1791 |
|
|
2003-03-26 20:49 gezelter |
1792 |
|
|
|
1793 |
|
|
* libmdtools/: DumpWriter.cpp, InitializeFromFile.cpp: Fixes to |
1794 |
|
|
fileio for MPI |
1795 |
|
|
|
1796 |
|
|
2003-03-26 18:14 gezelter |
1797 |
|
|
|
1798 |
|
|
* libmdtools/: DumpWriter.cpp, Exclude.cpp, Molecule.hpp, |
1799 |
|
|
mpiSimulation.cpp, mpiSimulation.hpp, mpiSimulation_module.F90: bug |
1800 |
|
|
fixes many bug fixes |
1801 |
|
|
|
1802 |
|
|
2003-03-26 17:24 gezelter |
1803 |
|
|
|
1804 |
|
|
* libmdtools/DumpWriter.cpp: Making DumpWriter less dependent on |
1805 |
|
|
sequence of atoms on the other processors. Node 0 now fires |
1806 |
|
|
potatoes at other processors to get them to send french fries back. |
1807 |
|
|
|
1808 |
|
|
2003-03-26 17:02 mmeineke |
1809 |
|
|
|
1810 |
|
|
* libmdtools/: DirectionalAtom.cpp, SimSetup.cpp: the skeleton for |
1811 |
|
|
making the molecules is in place. ForceField needs to be updated |
1812 |
|
|
next. |
1813 |
|
|
|
1814 |
|
|
2003-03-26 16:54 mmeineke |
1815 |
|
|
|
1816 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp, Exclude.cpp: fixed a couple of |
1817 |
|
|
the "static" bugs in Atom and Exclude |
1818 |
|
|
|
1819 |
|
|
2003-03-26 16:50 mmeineke |
1820 |
|
|
|
1821 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp, Molecule.hpp, SimInfo.hpp, |
1822 |
|
|
SimSetup.cpp: still working on the SimSetup routine. also fixed |
1823 |
|
|
some things in Exclude.hpp |
1824 |
|
|
|
1825 |
|
|
2003-03-26 16:24 gezelter |
1826 |
|
|
|
1827 |
|
|
* libmdtools/Makefile: Added Atom.cpp and Exclude.cpp |
1828 |
|
|
|
1829 |
|
|
2003-03-26 16:23 gezelter |
1830 |
|
|
|
1831 |
|
|
* libmdtools/: Atom.cpp, Exclude.cpp, Exclude.hpp: Fixes in Atom |
1832 |
|
|
and Exclude list |
1833 |
|
|
|
1834 |
|
|
2003-03-26 16:04 gezelter |
1835 |
|
|
|
1836 |
|
|
* libmdtools/: Atom.cpp, Atom.hpp: Make Atom.cpp able to add and |
1837 |
|
|
delete ranges of atoms |
1838 |
|
|
|
1839 |
|
|
2003-03-26 15:45 mmeineke |
1840 |
|
|
|
1841 |
|
|
* libmdtools/: Exclude.cpp, Exclude.hpp: added an Exclude class |
1842 |
|
|
with static arrays similar to the Atom class |
1843 |
|
|
|
1844 |
|
|
2003-03-26 15:22 mmeineke |
1845 |
|
|
|
1846 |
|
|
* libmdtools/: Molecule.hpp, SimSetup.cpp, SimSetup.hpp: I'm |
1847 |
|
|
overhauling the molecule class to contain it's own bonds, bends, |
1848 |
|
|
and torsions. |
1849 |
|
|
|
1850 |
|
|
may god have mercy on my soul. |
1851 |
|
|
|
1852 |
|
|
2003-03-26 14:34 chuckv |
1853 |
|
|
|
1854 |
|
|
* libmdtools/mpiSimulation.cpp: Finished globalIndex. |
1855 |
|
|
|
1856 |
|
|
2003-03-26 13:02 gezelter |
1857 |
|
|
|
1858 |
|
|
* libmdtools/: mpiComponentPlan.h, mpiSimulation.cpp, |
1859 |
|
|
mpiSimulation.hpp: MPI stuff for passing out molecules |
1860 |
|
|
|
1861 |
|
|
2003-03-26 11:12 chuckv |
1862 |
|
|
|
1863 |
|
|
* libmdtools/mpiSimulation.cpp: working on load balancing |
1864 |
|
|
|
1865 |
|
|
2003-03-26 10:37 chuckv |
1866 |
|
|
|
1867 |
|
|
* libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
1868 |
|
|
samples/argon/argon.bass: Fixes for Parallel thermalization |
1869 |
|
|
|
1870 |
|
|
2003-03-26 09:55 mmeineke |
1871 |
|
|
|
1872 |
|
|
* libmdtools/: SimInfo.cpp, Thermo.cpp: fixed an mpi include bug in |
1873 |
|
|
THermo.cpp |
1874 |
|
|
|
1875 |
|
|
2003-03-25 17:54 chuckv |
1876 |
|
|
|
1877 |
|
|
* libmdtools/: Thermo.cpp, Thermo.hpp: Fixed bugs with calculation |
1878 |
|
|
of potential energy and temperature. |
1879 |
|
|
|
1880 |
|
|
2003-03-25 09:29 mmeineke |
1881 |
|
|
|
1882 |
|
|
* libBASS/obj/dummy, libmdtools/MPIobj/dummy, libmdtools/obj/dummy, |
1883 |
|
|
src/MPIobj/dummy, src/obj/dummy: [no log message] |
1884 |
|
|
|
1885 |
|
|
2003-03-25 09:29 mmeineke |
1886 |
|
|
|
1887 |
|
|
* libBASS/MPIobj/dummy: added dummy files to keep the build |
1888 |
|
|
deirectories from being pruned. |
1889 |
|
|
|
1890 |
|
|
2003-03-24 20:07 gezelter |
1891 |
|
|
|
1892 |
gezelter |
760 |
* samples/Makefile, tests/Makefile: moving tests to samples |
1893 |
mmeineke |
568 |
|
1894 |
|
|
2003-03-24 20:06 gezelter |
1895 |
|
|
|
1896 |
gezelter |
760 |
* samples/alkane/Makefile, samples/alkane/alkanes.mdl, |
1897 |
|
|
samples/alkane/butane.bass, samples/alkane/init_butane.eor, |
1898 |
|
|
samples/argon/Makefile, samples/argon/argon.bass, |
1899 |
|
|
samples/argon/init_argon.eor, samples/argon/lj.mdl, |
1900 |
|
|
samples/lipid/5x5.bass, samples/lipid/Makefile, |
1901 |
|
|
samples/lipid/init_5x5.eor, samples/lipid/lipid.mdl, |
1902 |
|
|
samples/lipid/water.mdl, samples/water/Makefile, |
1903 |
|
|
samples/water/init_ssd.eor, samples/water/ssd.bass, |
1904 |
|
|
samples/water/water.mdl, tests/alkane/Makefile, |
1905 |
|
|
tests/alkane/alkanes.mdl, tests/alkane/butane.bass, |
1906 |
|
|
tests/alkane/init_butane.eor, tests/argon/Makefile, |
1907 |
|
|
tests/argon/argon.bass, tests/argon/init_argon.eor, |
1908 |
|
|
tests/argon/lj.mdl, tests/lipid/5x5.bass, tests/lipid/Makefile, |
1909 |
|
|
tests/lipid/init_5x5.eor, tests/lipid/lipid.mdl, |
1910 |
|
|
tests/lipid/water.mdl, tests/water/Makefile, |
1911 |
|
|
tests/water/init_ssd.eor, tests/water/ssd.bass, |
1912 |
|
|
tests/water/water.mdl: moved tests to samples |
1913 |
mmeineke |
568 |
|
1914 |
|
|
2003-03-24 19:51 gezelter |
1915 |
|
|
|
1916 |
|
|
* ac-tools/configure.in: Tests are becoming samples |
1917 |
|
|
|
1918 |
|
|
2003-03-24 19:46 gezelter |
1919 |
|
|
|
1920 |
gezelter |
760 |
* ac-tools/Make.conf.in, tests/Makefile, tests/alkane/Makefile, |
1921 |
|
|
tests/argon/Makefile, tests/lipid/Makefile, tests/water/Makefile: |
1922 |
|
|
Added makefiles in tests directories |
1923 |
mmeineke |
568 |
|
1924 |
|
|
2003-03-24 16:55 gezelter |
1925 |
|
|
|
1926 |
|
|
* libBASS/Globals.cpp, libBASS/Globals.hpp, libmdtools/SimInfo.cpp, |
1927 |
|
|
libmdtools/SimInfo.hpp, libmdtools/SimSetup.cpp, |
1928 |
|
|
libmdtools/TraPPE_ExFF.cpp, libmdtools/calc_dipole_dipole.F90, |
1929 |
|
|
libmdtools/calc_reaction_field.F90, |
1930 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
1931 |
|
|
libmdtools/simulation_module.F90: electrostatic changes for dipole |
1932 |
|
|
/ RF separation |
1933 |
|
|
|
1934 |
|
|
2003-03-24 13:33 mmeineke |
1935 |
|
|
|
1936 |
|
|
* libmdtools/: Atom.hpp, ForceFields.cpp, SimInfo.cpp, |
1937 |
|
|
do_Forces.F90: little bug fixes here and there |
1938 |
|
|
|
1939 |
gezelter |
760 |
2003-03-24 11:04 mmeineke |
1940 |
|
|
|
1941 |
|
|
* tests/argon/: argon.bass, init_argon.eor, lj.mdl: added an argon |
1942 |
|
|
test simulation |
1943 |
|
|
|
1944 |
|
|
2003-03-24 11:02 mmeineke |
1945 |
|
|
|
1946 |
|
|
* tests/: lipid/5x5.bass, lipid/init_5x5.eor, lipid/lipid.mdl, |
1947 |
|
|
lipid/water.mdl, water/init_ssd.eor, water/ssd.bass, |
1948 |
|
|
water/water.mdl: [no log message] |
1949 |
|
|
|
1950 |
|
|
2003-03-24 11:02 mmeineke |
1951 |
|
|
|
1952 |
|
|
* tests/alkane/: alkanes.mdl, butane.bass, init_butane.eor: added |
1953 |
|
|
some test bass files for experimenting with |
1954 |
|
|
|
1955 |
mmeineke |
568 |
2003-03-24 10:26 mmeineke |
1956 |
|
|
|
1957 |
|
|
* libmdtools/: ForceFields.cpp, f_verlet_constrained.F90: fixed bug |
1958 |
|
|
where short range interactions were not being calculated. |
1959 |
|
|
|
1960 |
|
|
removed some debug print statements |
1961 |
|
|
|
1962 |
|
|
2003-03-21 17:11 chuckv |
1963 |
|
|
|
1964 |
|
|
* libmdtools/: TraPPE_ExFF.cpp, calc_dipole_dipole.F90, |
1965 |
|
|
do_Forces.F90, f_verlet_constrained.F90, simulation_module.F90: |
1966 |
|
|
various write statements for debugging |
1967 |
|
|
|
1968 |
|
|
2003-03-21 16:26 chuckv |
1969 |
|
|
|
1970 |
|
|
* forceFields/Makefile: added links to the makefile in forceFields |
1971 |
|
|
|
1972 |
|
|
2003-03-21 15:52 gezelter |
1973 |
|
|
|
1974 |
|
|
* ac-tools/Make.conf.in, ac-tools/configure.in, |
1975 |
|
|
libmdtools/Makefile: Fixed F_MACH_DEP bug |
1976 |
|
|
|
1977 |
|
|
2003-03-21 15:37 gezelter |
1978 |
|
|
|
1979 |
|
|
* ChangeLog, Makefile, ac-tools/Make.conf.in, ac-tools/config.h.in, |
1980 |
|
|
ac-tools/configure.in, forceFields/Makefile, libBASS/Makefile, |
1981 |
|
|
libmdtools/Makefile, scripts/cvs2cl.pl, scripts/sfmakedepend, |
1982 |
|
|
src/Makefile, utils/sfmakedepend: Makefile fixes, directory re-org, |
1983 |
|
|
autoconf fixes |
1984 |
|
|
|
1985 |
gezelter |
385 |
2003-03-21 14:58 gezelter |
1986 |
mmeineke |
377 |
|
1987 |
gezelter |
385 |
* LICENSE: Added license file |
1988 |
|
|
|
1989 |
|
|
2003-03-21 14:55 gezelter |
1990 |
|
|
|
1991 |
|
|
* forceFields/Makefile: Fixed makefile |
1992 |
|
|
|
1993 |
|
|
2003-03-21 14:49 gezelter |
1994 |
|
|
|
1995 |
|
|
* forceFields/Makefile: Makefile for forceFields |
1996 |
|
|
|
1997 |
|
|
2003-03-21 14:42 gezelter |
1998 |
|
|
|
1999 |
|
|
* README: Readme changes |
2000 |
|
|
|
2001 |
|
|
2003-03-21 12:52 mmeineke |
2002 |
|
|
|
2003 |
|
|
* src/Makefile: [no log message] |
2004 |
|
|
|
2005 |
|
|
2003-03-21 12:52 mmeineke |
2006 |
|
|
|
2007 |
|
|
* libBASS/Makefile, libmdtools/Makefile: Makefile fixes for depends |
2008 |
|
|
|
2009 |
|
|
2003-03-21 12:42 mmeineke |
2010 |
|
|
|
2011 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
2012 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
2013 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
2014 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
2015 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
2016 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
2017 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
2018 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
2019 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
2020 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
2021 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
2022 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
2023 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
2024 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
2025 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
2026 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
2027 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
2028 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
2029 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
2030 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
2031 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
2032 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
2033 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
2034 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
2035 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
2036 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
2037 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
2038 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
2039 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
2040 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
2041 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
2042 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
2043 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
2044 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
2045 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
2046 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
2047 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
2048 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
2049 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
2050 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
2051 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
2052 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
2053 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
2054 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
2055 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
2056 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
2057 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
2058 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
2059 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
2060 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
2061 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
2062 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
2063 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
2064 |
tim |
837 |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: New OOPSE |
2065 |
|
|
Tree |
2066 |
gezelter |
385 |
|
2067 |
|
|
2003-03-21 12:42 mmeineke |
2068 |
|
|
|
2069 |
|
|
* AUTHORS, ChangeLog, NEWS, Makefile, README, |
2070 |
|
|
ac-tools/Make.conf.in, ac-tools/aclocal.m4, ac-tools/config.guess, |
2071 |
|
|
ac-tools/config.h.in, ac-tools/config.sub, ac-tools/configure.in, |
2072 |
|
|
ac-tools/install-sh, forceFields/DipoleTest.frc, |
2073 |
|
|
forceFields/LJ_FF.frc, forceFields/TraPPE.frc, |
2074 |
|
|
forceFields/TraPPE_Ex.frc, libBASS/AtomStamp.cpp, |
2075 |
|
|
libBASS/AtomStamp.hpp, libBASS/BASS_interface.cpp, |
2076 |
|
|
libBASS/BASS_interface.h, libBASS/BASS_parse.c, |
2077 |
|
|
libBASS/BASS_parse.h, libBASS/BASSlex.l, libBASS/BASSyacc.y, |
2078 |
|
|
libBASS/BendStamp.cpp, libBASS/BendStamp.hpp, |
2079 |
|
|
libBASS/BondStamp.cpp, libBASS/BondStamp.hpp, |
2080 |
|
|
libBASS/Component.cpp, libBASS/Component.hpp, libBASS/Globals.cpp, |
2081 |
|
|
libBASS/Globals.hpp, libBASS/LinkedAssign.cpp, |
2082 |
|
|
libBASS/LinkedAssign.hpp, libBASS/LinkedCommand.cpp, |
2083 |
|
|
libBASS/LinkedCommand.hpp, libBASS/MakeStamps.cpp, |
2084 |
|
|
libBASS/MakeStamps.hpp, libBASS/Makefile, |
2085 |
|
|
libBASS/MoleculeStamp.cpp, libBASS/MoleculeStamp.hpp, |
2086 |
|
|
libBASS/TorsionStamp.cpp, libBASS/TorsionStamp.hpp, |
2087 |
|
|
libBASS/interface.c, libBASS/make_nodes.c, libBASS/make_nodes.h, |
2088 |
|
|
libBASS/mpiBASS.c, libBASS/mpiBASS.h, libBASS/node_list.h, |
2089 |
|
|
libBASS/parse_interface.h, libBASS/parse_me.h, |
2090 |
|
|
libBASS/parse_tree.c, libBASS/parse_tree.h, libBASS/simError.c, |
2091 |
|
|
libBASS/simError.h, src/Makefile, src/oopse.cpp, src/oose.cpp, |
2092 |
|
|
utils/sfmakedepend, ac-tools/shtool, |
2093 |
|
|
libmdtools/AbstractClasses.hpp, libmdtools/Atom.hpp, |
2094 |
|
|
libmdtools/Bend.cpp, libmdtools/BendExtensions.cpp, |
2095 |
|
|
libmdtools/Bond.cpp, libmdtools/BondExtensions.cpp, |
2096 |
|
|
libmdtools/DipoleTestFF.cpp, libmdtools/DirectionalAtom.cpp, |
2097 |
|
|
libmdtools/DumpWriter.cpp, libmdtools/ForceFields.cpp, |
2098 |
|
|
libmdtools/ForceFields.hpp, libmdtools/GhostBend.cpp, |
2099 |
|
|
libmdtools/InitializeFromFile.cpp, libmdtools/Integrator.hpp, |
2100 |
|
|
libmdtools/LJ_FF.cpp, libmdtools/Linux_ifc_machdep.F90, |
2101 |
|
|
libmdtools/Makefile, libmdtools/Molecule.hpp, |
2102 |
|
|
libmdtools/ReadWrite.hpp, libmdtools/SRI.hpp, |
2103 |
|
|
libmdtools/SimInfo.cpp, libmdtools/SimInfo.hpp, |
2104 |
|
|
libmdtools/SimSetup.cpp, libmdtools/SimSetup.hpp, |
2105 |
|
|
libmdtools/StatWriter.cpp, libmdtools/Symplectic.cpp, |
2106 |
|
|
libmdtools/Thermo.cpp, libmdtools/Thermo.hpp, |
2107 |
|
|
libmdtools/Torsion.cpp, libmdtools/TorsionExtensions.cpp, |
2108 |
|
|
libmdtools/TraPPEFF.cpp, libmdtools/TraPPE_ExFF.cpp, |
2109 |
|
|
libmdtools/Verlet.cpp, libmdtools/atype_module.F90, |
2110 |
|
|
libmdtools/calc_LJ_FF.F90, libmdtools/calc_dipole_dipole.F90, |
2111 |
|
|
libmdtools/calc_gb.F90, libmdtools/calc_reaction_field.F90, |
2112 |
|
|
libmdtools/calc_sticky_pair.F90, libmdtools/do_Forces.F90, |
2113 |
|
|
libmdtools/fForceField.h, libmdtools/fSimulation.h, |
2114 |
|
|
libmdtools/f_verlet_constrained.F90, libmdtools/forceFactory.hpp, |
2115 |
|
|
libmdtools/force_globals.F90, libmdtools/fortranWrapDefines.hpp, |
2116 |
|
|
libmdtools/fortranWrappers.cpp, libmdtools/fortranWrappers.hpp, |
2117 |
|
|
libmdtools/mpiComponentPlan.h, libmdtools/mpiForceField.c, |
2118 |
|
|
libmdtools/mpiForceField.h, libmdtools/mpiSimulation.cpp, |
2119 |
|
|
libmdtools/mpiSimulation.hpp, libmdtools/mpiSimulation_module.F90, |
2120 |
|
|
libmdtools/neighborLists.F90, libmdtools/randomSPRNG.cpp, |
2121 |
|
|
libmdtools/randomSPRNG.hpp, libmdtools/simulation_module.F90, |
2122 |
tim |
837 |
libmdtools/vector_class.F90, libmdtools/wrappers.F90: Initial |
2123 |
|
|
revision |
2124 |
gezelter |
385 |
|