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Comparing:
trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents), Revision 1098 by chuckv, Thu Dec 14 19:38:56 2006 UTC vs.
branches/development/src/applications/dynamicProps/DynamicProps.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include <iostream>
# Line 46 | Line 47
47   #include "brains/Register.hpp"
48   #include "brains/SimCreator.hpp"
49   #include "brains/SimInfo.hpp"
50 + #include "utils/StringUtils.hpp"
51   #include "utils/simError.h"
52  
53   #include "applications/dynamicProps/DynamicPropsCmd.h"
# Line 54 | Line 56
56   #include "applications/dynamicProps/VCorrFunc.hpp"
57   #include "applications/dynamicProps/LegendreCorrFunc.hpp"
58   #include "applications/dynamicProps/RadialRCorrFunc.hpp"
59 + #include "applications/dynamicProps/ThetaCorrFunc.hpp"
60 + #include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
61 + #include "applications/dynamicProps/EnergyCorrFunc.hpp"
62 + #include "applications/dynamicProps/StressCorrFunc.hpp"
63 + #include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
64 + #include "applications/dynamicProps/MomentumCorrFunc.hpp"
65  
66  
59 – using namespace oopse;
67  
68 + using namespace OpenMD;
69 +
70   int main(int argc, char* argv[]){
71    
72    //register force fields
# Line 80 | Line 89 | int main(int argc, char* argv[]){
89    if (args_info.sele1_given) {
90      sele1 = args_info.sele1_arg;
91    }else {
92 <    char*  sele1Env= getenv("OOPSE_SELE1");
92 >    char*  sele1Env= getenv("SELECTION1");
93      if (sele1Env) {
94        sele1 = sele1Env;
95      }else {
96        sprintf( painCave.errMsg,
97 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
98 <      painCave.severity = OOPSE_ERROR;
97 >               "neither --sele1 option nor $SELECTION1 is set");
98 >      painCave.severity = OPENMD_ERROR;
99        painCave.isFatal = 1;
100        simError();
101      }
# Line 95 | Line 104 | int main(int argc, char* argv[]){
104    if (args_info.sele2_given) {
105      sele2 = args_info.sele2_arg;
106    }else {
107 <    char* sele2Env = getenv("OOPSE_SELE2");
107 >    char* sele2Env = getenv("SELECTION2");
108      if (sele2Env) {
109        sele2 = sele2Env;            
110      } else {
# Line 103 | Line 112 | int main(int argc, char* argv[]){
112      }
113    }
114  
115 +  // use the memory string to figure out how much memory we can use:
116 +  char *end;
117 +  long long int memSize = memparse(args_info.memory_arg, &end);
118 +  sprintf( painCave.errMsg,
119 +           "Amount of memory being used: %llu bytes\n", memSize);
120 +  painCave.severity = OPENMD_INFO;
121 +  painCave.isFatal = 0;
122 +  simError();    
123 +
124    //parse md file and set up the system
125    SimCreator creator;
126    SimInfo* info = creator.createSim(dumpFileName, false);
127  
128  
129    TimeCorrFunc* corrFunc;
130 <  if (args_info.dcorr_given){
131 <    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
130 >  if(args_info.sdcorr_given){
131 >    corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132 >  } else if (args_info.dcorr_given){
133 >    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134    } else if (args_info.rcorr_given) {
135 <    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
135 >    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136    } else if (args_info.r_rcorr_given) {
137 <    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
138 <  }
139 <  else if (args_info.vcorr_given) {
140 <    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
137 >    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
138 >  } else if (args_info.thetacorr_given) {
139 >    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
140 >  } else if (args_info.drcorr_given) {
141 >    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
142 >  } else if (args_info.vcorr_given) {
143 >    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
144 >  } else if (args_info.helfandEcorr_given){
145 >    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
146 >  } else if (args_info.stresscorr_given){
147 >    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
148 >  } else if (args_info.momentum_given){
149 >    corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
150    } else if (args_info.lcorr_given) {
151      int order;
152      if (args_info.order_given)
# Line 125 | Line 154 | int main(int argc, char* argv[]){
154      else {
155        sprintf( painCave.errMsg,
156                 "--order must be set if --lcoor is set\n");
157 <      painCave.severity = OOPSE_ERROR;
157 >      painCave.severity = OPENMD_ERROR;
158        painCave.isFatal = 1;
159        simError();
160      }
161          
162 <    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
162 >    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
163    }
164  
165    if (args_info.output_given) {

Comparing:
trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords), Revision 1098 by chuckv, Thu Dec 14 19:38:56 2006 UTC vs.
branches/development/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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1 + Author Id Revision Date

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