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Comparing:
trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents), Revision 1112 by chuckv, Wed Jan 3 20:47:00 2007 UTC vs.
branches/development/src/applications/dynamicProps/DynamicProps.cpp (file contents), Revision 1629 by gezelter, Wed Sep 14 21:15:17 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 55 | Line 56
56   #include "applications/dynamicProps/LegendreCorrFunc.hpp"
57   #include "applications/dynamicProps/RadialRCorrFunc.hpp"
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  
60 – using namespace oopse;
66  
67 + using namespace OpenMD;
68 +
69   int main(int argc, char* argv[]){
70    
71    //register force fields
# Line 81 | Line 88 | int main(int argc, char* argv[]){
88    if (args_info.sele1_given) {
89      sele1 = args_info.sele1_arg;
90    }else {
91 <    char*  sele1Env= getenv("OOPSE_SELE1");
91 >    char*  sele1Env= getenv("SELECTION1");
92      if (sele1Env) {
93        sele1 = sele1Env;
94      }else {
95        sprintf( painCave.errMsg,
96 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
97 <      painCave.severity = OOPSE_ERROR;
96 >               "neither --sele1 option nor $SELECTION1 is set");
97 >      painCave.severity = OPENMD_ERROR;
98        painCave.isFatal = 1;
99        simError();
100      }
# Line 96 | Line 103 | int main(int argc, char* argv[]){
103    if (args_info.sele2_given) {
104      sele2 = args_info.sele2_arg;
105    }else {
106 <    char* sele2Env = getenv("OOPSE_SELE2");
106 >    char* sele2Env = getenv("SELECTION2");
107      if (sele2Env) {
108        sele2 = sele2Env;            
109      } else {
# Line 104 | Line 111 | int main(int argc, char* argv[]){
111      }
112    }
113  
114 +  // use the memory string to figure out how much memory we can use:
115 +  char *end;
116 +  long long int memSize = memparse(args_info.memory_arg, &end);
117 +  sprintf( painCave.errMsg,
118 +           "Amount of memory being used: %llu bytes\n", memSize);
119 +  painCave.severity = OPENMD_INFO;
120 +  painCave.isFatal = 0;
121 +  simError();    
122 +
123    //parse md file and set up the system
124    SimCreator creator;
125    SimInfo* info = creator.createSim(dumpFileName, false);
126  
127  
128    TimeCorrFunc* corrFunc;
129 <  if (args_info.dcorr_given){
130 <    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
129 >  if(args_info.sdcorr_given){
130 >    corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
131 >  } else if (args_info.dcorr_given){
132 >    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
133    } else if (args_info.rcorr_given) {
134 <    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
134 >    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
135    } else if (args_info.r_rcorr_given) {
136 <    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
136 >    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
137    } else if (args_info.thetacorr_given) {
138 <    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
139 <  }
140 <  else if (args_info.vcorr_given) {
141 <    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
138 >    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
139 >  } else if (args_info.drcorr_given) {
140 >    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
141 >  } else if (args_info.vcorr_given) {
142 >    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
143 >  } else if (args_info.helfandEcorr_given){
144 >    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
145 >  } else if (args_info.stresscorr_given){
146 >    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
147 >  } else if (args_info.momentum_given){
148 >    corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
149    } else if (args_info.lcorr_given) {
150      int order;
151      if (args_info.order_given)
# Line 128 | Line 153 | int main(int argc, char* argv[]){
153      else {
154        sprintf( painCave.errMsg,
155                 "--order must be set if --lcoor is set\n");
156 <      painCave.severity = OOPSE_ERROR;
156 >      painCave.severity = OPENMD_ERROR;
157        painCave.isFatal = 1;
158        simError();
159      }
160          
161 <    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
161 >    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
162    }
163  
164    if (args_info.output_given) {

Comparing:
trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords), Revision 1112 by chuckv, Wed Jan 3 20:47:00 2007 UTC vs.
branches/development/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

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1 + Author Id Revision Date

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