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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 1596 by gezelter, Mon Jul 25 17:30:53 2011 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 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 + #include "applications/dynamicProps/cOHz.hpp"
67 + #include "applications/dynamicProps/BondCorrFunc.hpp"
68  
63 –
69   using namespace OpenMD;
70  
71   int main(int argc, char* argv[]){
72    
68 –  //register force fields
69 –  registerForceFields();
70 –
73    gengetopt_args_info args_info;
74  
75    //parse the command line option
# Line 75 | Line 77 | int main(int argc, char* argv[]){
77      exit(1) ;
78    }
79  
78 –
80    //get the dumpfile name and meta-data file name
81    std::string dumpFileName = args_info.input_arg;
82      
83    std::string sele1;
84    std::string sele2;
85 <
85 >  
86 >  // check the first selection argument, or set it to the environment
87 >  // variable, or failing that, set it to "select all"
88 >  
89    if (args_info.sele1_given) {
90      sele1 = args_info.sele1_arg;
91 <  }else {
91 >  } else {
92      char*  sele1Env= getenv("SELECTION1");
93      if (sele1Env) {
94        sele1 = sele1Env;
95 <    }else {
96 <      sprintf( painCave.errMsg,
93 <               "neither --sele1 option nor $SELECTION1 is set");
94 <      painCave.severity = OPENMD_ERROR;
95 <      painCave.isFatal = 1;
96 <      simError();
95 >    } else {
96 >      sele1 = "select all";
97      }
98    }
99 <    
99 >  
100 >  // check the second selection argument, or set it to the environment
101 >  // variable, or failing that, set it to the first selection
102 >  
103    if (args_info.sele2_given) {
104      sele2 = args_info.sele2_arg;
105 <  }else {
105 >  } else {
106      char* sele2Env = getenv("SELECTION2");
107      if (sele2Env) {
108        sele2 = sele2Env;            
109 <    } else {
109 >    } else {
110 >      //If sele2 is not specified, then the default behavior
111 >      //should be what is already intended for sele1
112        sele2 = sele1;
113      }
114    }
# Line 115 | Line 120 | int main(int argc, char* argv[]){
120             "Amount of memory being used: %llu bytes\n", memSize);
121    painCave.severity = OPENMD_INFO;
122    painCave.isFatal = 0;
123 <  simError();
124 <    
123 >  simError();    
124 >
125    //parse md file and set up the system
126    SimCreator creator;
127    SimInfo* info = creator.createSim(dumpFileName, false);
128  
124 –
129    TimeCorrFunc* corrFunc;
130 <  if (args_info.dcorr_given){
130 >  if(args_info.sdcorr_given){
131 >    corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132 >  } else if (args_info.selecorr_given){
133 >    corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134 >  } else if (args_info.dcorr_given){
135      corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136    } else if (args_info.rcorr_given) {
137      corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
# Line 135 | Line 143 | int main(int argc, char* argv[]){
143      corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
144    } else if (args_info.vcorr_given) {
145      corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
146 +  } else if (args_info.bondcorr_given) {
147 +    corrFunc = new BondCorrFunc(info, dumpFileName, sele1, memSize);
148    } else if (args_info.helfandEcorr_given){
149      corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
150    } else if (args_info.stresscorr_given){
151      corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
152 +  } else if (args_info.momentum_given){
153 +    corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
154    } else if (args_info.lcorr_given) {
155      int order;
156      if (args_info.order_given)
157          order = args_info.order_arg;
158      else {
159        sprintf( painCave.errMsg,
160 <               "--order must be set if --lcoor is set\n");
160 >               "--order must be set if --lcorr is set\n");
161        painCave.severity = OPENMD_ERROR;
162        painCave.isFatal = 1;
163        simError();
164      }
165          
166      corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
167 +  } else if (args_info.lcorrZ_given) {
168 +    int order;
169 +    if (args_info.order_given)
170 +        order = args_info.order_arg;
171 +    else {
172 +      sprintf( painCave.errMsg,
173 +               "--order must be set if --lcorrZ is set\n");
174 +      painCave.severity = OPENMD_ERROR;
175 +      painCave.isFatal = 1;
176 +      simError();
177 +    }
178 +        
179 +    corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
180 +
181 +  } else if (args_info.cohZ_given) {
182 +    int order;
183 +    if (args_info.order_given)
184 +        order = args_info.order_arg;
185 +    else {
186 +      sprintf( painCave.errMsg,
187 +               "--order must be set if --cohZ is set\n");
188 +      painCave.severity = OPENMD_ERROR;
189 +      painCave.isFatal = 1;
190 +      simError();
191 +    }
192 +        
193 +    corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
194 +
195    }
196  
197 +
198    if (args_info.output_given) {
199      corrFunc->setOutputName(args_info.output_arg);
200    }

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