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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 1615 by gezelter, Fri Aug 26 17:55:44 2011 UTC vs.
Revision 1934 by gezelter, Mon Aug 26 14:15:09 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"
# Line 61 | Line 63
63   #include "applications/dynamicProps/StressCorrFunc.hpp"
64   #include "applications/dynamicProps/SystemDipoleCorrFunc.hpp"
65   #include "applications/dynamicProps/MomentumCorrFunc.hpp"
66 + #include "applications/dynamicProps/cOHz.hpp"
67  
65 –
68   using namespace OpenMD;
69  
70   int main(int argc, char* argv[]){
71    
70 –  //register force fields
71 –  registerForceFields();
72 –
72    gengetopt_args_info args_info;
73  
74    //parse the command line option
# Line 101 | Line 100 | int main(int argc, char* argv[]){
100      
101    if (args_info.sele2_given) {
102      sele2 = args_info.sele2_arg;
103 <  }else {
103 >  } else {
104      char* sele2Env = getenv("SELECTION2");
105      if (sele2Env) {
106        sele2 = sele2Env;            
# Line 117 | Line 116 | int main(int argc, char* argv[]){
116             "Amount of memory being used: %llu bytes\n", memSize);
117    painCave.severity = OPENMD_INFO;
118    painCave.isFatal = 0;
119 <  simError();
120 <    
119 >  simError();    
120 >
121    //parse md file and set up the system
122    SimCreator creator;
123    SimInfo* info = creator.createSim(dumpFileName, false);
124  
126 –
125    TimeCorrFunc* corrFunc;
126    if(args_info.sdcorr_given){
127      corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
128 +  } else if (args_info.selecorr_given){
129 +    corrFunc = new SelectionCorrFunc(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) {
# Line 151 | Line 151 | int main(int argc, char* argv[]){
151          order = args_info.order_arg;
152      else {
153        sprintf( painCave.errMsg,
154 <               "--order must be set if --lcoor is set\n");
154 >               "--order must be set if --lcorr is set\n");
155        painCave.severity = OPENMD_ERROR;
156        painCave.isFatal = 1;
157        simError();
158      }
159          
160      corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
161 +  } else if (args_info.lcorrZ_given) {
162 +    int order;
163 +    if (args_info.order_given)
164 +        order = args_info.order_arg;
165 +    else {
166 +      sprintf( painCave.errMsg,
167 +               "--order must be set if --lcorrZ is set\n");
168 +      painCave.severity = OPENMD_ERROR;
169 +      painCave.isFatal = 1;
170 +      simError();
171 +    }
172 +        
173 +    corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
174 +
175 +  } else if (args_info.cohZ_given) {
176 +    int order;
177 +    if (args_info.order_given)
178 +        order = args_info.order_arg;
179 +    else {
180 +      sprintf( painCave.errMsg,
181 +               "--order must be set if --cohZ is set\n");
182 +      painCave.severity = OPENMD_ERROR;
183 +      painCave.isFatal = 1;
184 +      simError();
185 +    }
186 +        
187 +    corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
188 +
189    }
190  
191 +
192 +
193    if (args_info.output_given) {
194      corrFunc->setOutputName(args_info.output_arg);
195    }

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