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Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 1245 by chuckv, Tue May 27 16:39:06 2008 UTC vs.
Revision 1615 by gezelter, Fri Aug 26 17:55:44 2011 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include <iostream>
# Line 46 | Line 46
46   #include "brains/Register.hpp"
47   #include "brains/SimCreator.hpp"
48   #include "brains/SimInfo.hpp"
49 + #include "utils/StringUtils.hpp"
50   #include "utils/simError.h"
51  
52   #include "applications/dynamicProps/DynamicPropsCmd.h"
# Line 57 | Line 58
58   #include "applications/dynamicProps/ThetaCorrFunc.hpp"
59   #include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
60   #include "applications/dynamicProps/EnergyCorrFunc.hpp"
61 + #include "applications/dynamicProps/StressCorrFunc.hpp"
62 + #include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
63 + #include "applications/dynamicProps/MomentumCorrFunc.hpp"
64  
65  
66 < using namespace oopse;
66 > using namespace OpenMD;
67  
68   int main(int argc, char* argv[]){
69    
# Line 83 | Line 87 | int main(int argc, char* argv[]){
87    if (args_info.sele1_given) {
88      sele1 = args_info.sele1_arg;
89    }else {
90 <    char*  sele1Env= getenv("OOPSE_SELE1");
90 >    char*  sele1Env= getenv("SELECTION1");
91      if (sele1Env) {
92        sele1 = sele1Env;
93      }else {
94        sprintf( painCave.errMsg,
95 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
96 <      painCave.severity = OOPSE_ERROR;
95 >               "neither --sele1 option nor $SELECTION1 is set");
96 >      painCave.severity = OPENMD_ERROR;
97        painCave.isFatal = 1;
98        simError();
99      }
# Line 98 | Line 102 | int main(int argc, char* argv[]){
102    if (args_info.sele2_given) {
103      sele2 = args_info.sele2_arg;
104    }else {
105 <    char* sele2Env = getenv("OOPSE_SELE2");
105 >    char* sele2Env = getenv("SELECTION2");
106      if (sele2Env) {
107        sele2 = sele2Env;            
108      } else {
# Line 106 | Line 110 | int main(int argc, char* argv[]){
110      }
111    }
112  
113 +  // use the memory string to figure out how much memory we can use:
114 +  char *end;
115 +  long long int memSize = memparse(args_info.memory_arg, &end);
116 +  sprintf( painCave.errMsg,
117 +           "Amount of memory being used: %llu bytes\n", memSize);
118 +  painCave.severity = OPENMD_INFO;
119 +  painCave.isFatal = 0;
120 +  simError();
121 +    
122    //parse md file and set up the system
123    SimCreator creator;
124    SimInfo* info = creator.createSim(dumpFileName, false);
125  
126  
127    TimeCorrFunc* corrFunc;
128 <  if (args_info.dcorr_given){
129 <    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
128 >  if(args_info.sdcorr_given){
129 >    corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
130 >  } else if (args_info.dcorr_given){
131 >    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132    } else if (args_info.rcorr_given) {
133 <    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
133 >    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134    } else if (args_info.r_rcorr_given) {
135 <    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
135 >    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136    } else if (args_info.thetacorr_given) {
137 <    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
137 >    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
138    } else if (args_info.drcorr_given) {
139 <    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
139 >    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
140    } else if (args_info.vcorr_given) {
141 <    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
141 >    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
142    } else if (args_info.helfandEcorr_given){
143 <    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2);  
143 >    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
144 >  } else if (args_info.stresscorr_given){
145 >    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
146 >  } else if (args_info.momentum_given){
147 >    corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
148    } else if (args_info.lcorr_given) {
149      int order;
150      if (args_info.order_given)
# Line 133 | Line 152 | int main(int argc, char* argv[]){
152      else {
153        sprintf( painCave.errMsg,
154                 "--order must be set if --lcoor is set\n");
155 <      painCave.severity = OOPSE_ERROR;
155 >      painCave.severity = OPENMD_ERROR;
156        painCave.isFatal = 1;
157        simError();
158      }
159          
160 <    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
160 >    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
161    }
162  
163    if (args_info.output_given) {

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords):
Revision 1245 by chuckv, Tue May 27 16:39:06 2008 UTC vs.
Revision 1615 by gezelter, Fri Aug 26 17:55:44 2011 UTC

# Line 0 | Line 1
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