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root/OpenMD/trunk/src/applications/dynamicProps/DynamicProps.cpp
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Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 1604 by jmichalk, Mon Aug 8 18:53:40 2011 UTC vs.
Revision 1915 by gezelter, Mon Jul 29 17:55:17 2013 UTC

# Line 35 | Line 35
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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>
44   #include <fstream>
45   #include <string>
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"
53 + #include "applications/dynamicProps/SelectionCorrFunc.hpp"
54   #include "applications/dynamicProps/DipoleCorrFunc.hpp"
55   #include "applications/dynamicProps/RCorrFunc.hpp"
56   #include "applications/dynamicProps/VCorrFunc.hpp"
57   #include "applications/dynamicProps/LegendreCorrFunc.hpp"
58 + #include "applications/dynamicProps/LegendreCorrFuncZ.hpp"
59   #include "applications/dynamicProps/RadialRCorrFunc.hpp"
60   #include "applications/dynamicProps/ThetaCorrFunc.hpp"
61   #include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
62   #include "applications/dynamicProps/EnergyCorrFunc.hpp"
63   #include "applications/dynamicProps/StressCorrFunc.hpp"
64   #include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
65 + #include "applications/dynamicProps/MomentumCorrFunc.hpp"
66  
64 –
67   using namespace OpenMD;
68  
69   int main(int argc, char* argv[]){
70    
69 –  //register force fields
70 –  registerForceFields();
71 –
71    gengetopt_args_info args_info;
72  
73    //parse the command line option
# Line 100 | Line 99 | int main(int argc, char* argv[]){
99      
100    if (args_info.sele2_given) {
101      sele2 = args_info.sele2_arg;
102 <  }else {
102 >  } else {
103      char* sele2Env = getenv("SELECTION2");
104      if (sele2Env) {
105        sele2 = sele2Env;            
# Line 116 | Line 115 | int main(int argc, char* argv[]){
115             "Amount of memory being used: %llu bytes\n", memSize);
116    painCave.severity = OPENMD_INFO;
117    painCave.isFatal = 0;
118 <  simError();
119 <    
118 >  simError();    
119 >
120    //parse md file and set up the system
121    SimCreator creator;
122    SimInfo* info = creator.createSim(dumpFileName, false);
123  
125 –
124    TimeCorrFunc* corrFunc;
125    if(args_info.sdcorr_given){
126      corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
127 +  } else if (args_info.selecorr_given){
128 +    corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
129    } else if (args_info.dcorr_given){
130      corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
131    } else if (args_info.rcorr_given) {
# Line 142 | Line 142 | int main(int argc, char* argv[]){
142      corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
143    } else if (args_info.stresscorr_given){
144      corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
145 +  } else if (args_info.momentum_given){
146 +    corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
147    } else if (args_info.lcorr_given) {
148      int order;
149      if (args_info.order_given)
150          order = args_info.order_arg;
151      else {
152        sprintf( painCave.errMsg,
153 <               "--order must be set if --lcoor is set\n");
153 >               "--order must be set if --lcorr is set\n");
154        painCave.severity = OPENMD_ERROR;
155        painCave.isFatal = 1;
156        simError();
157      }
158          
159      corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
160 +  } else if (args_info.lcorrZ_given) {
161 +    int order;
162 +    if (args_info.order_given)
163 +        order = args_info.order_arg;
164 +    else {
165 +      sprintf( painCave.errMsg,
166 +               "--order must be set if --lcorrZ is set\n");
167 +      painCave.severity = OPENMD_ERROR;
168 +      painCave.isFatal = 1;
169 +      simError();
170 +    }
171 +        
172 +    corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
173 +
174    }
175  
176    if (args_info.output_given) {

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