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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 1937 by gezelter, Tue Oct 29 16:02:58 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 77 | Line 76 | int main(int argc, char* argv[]){
76      exit(1) ;
77    }
78  
80 –
79    //get the dumpfile name and meta-data file name
80    std::string dumpFileName = args_info.input_arg;
81      
82    std::string sele1;
83    std::string sele2;
84 <
84 >  
85 >  // check the first selection argument, or set it to the environment
86 >  // variable, or failing that, set it to "select all"
87 >  
88    if (args_info.sele1_given) {
89      sele1 = args_info.sele1_arg;
90 <  }else {
90 >  } else {
91      char*  sele1Env= getenv("SELECTION1");
92      if (sele1Env) {
93        sele1 = sele1Env;
94 <    }else {
95 <      sprintf( painCave.errMsg,
95 <               "neither --sele1 option nor $SELECTION1 is set");
96 <      painCave.severity = OPENMD_ERROR;
97 <      painCave.isFatal = 1;
98 <      simError();
94 >    } else {
95 >      sele1 = "select all";
96      }
97    }
98 <    
98 >  
99 >  // check the second selection argument, or set it to the environment
100 >  // variable, or failing that, set it to the first selection
101 >  
102    if (args_info.sele2_given) {
103      sele2 = args_info.sele2_arg;
104 <  }else {
104 >  } else {
105      char* sele2Env = getenv("SELECTION2");
106      if (sele2Env) {
107        sele2 = sele2Env;            
108 <    } else {
108 >    } else {
109 >      //If sele2 is not specified, then the default behavior
110 >      //should be what is already intended for sele1
111        sele2 = sele1;
112      }
113    }
# Line 117 | Line 119 | int main(int argc, char* argv[]){
119             "Amount of memory being used: %llu bytes\n", memSize);
120    painCave.severity = OPENMD_INFO;
121    painCave.isFatal = 0;
122 <  simError();
123 <    
122 >  simError();    
123 >
124    //parse md file and set up the system
125    SimCreator creator;
126    SimInfo* info = creator.createSim(dumpFileName, false);
127  
126 –
128    TimeCorrFunc* corrFunc;
129    if(args_info.sdcorr_given){
130      corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
131 +  } else if (args_info.selecorr_given){
132 +    corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
133    } else if (args_info.dcorr_given){
134      corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
135    } else if (args_info.rcorr_given) {
# Line 151 | Line 154 | int main(int argc, char* argv[]){
154          order = args_info.order_arg;
155      else {
156        sprintf( painCave.errMsg,
157 <               "--order must be set if --lcoor is set\n");
157 >               "--order must be set if --lcorr is set\n");
158        painCave.severity = OPENMD_ERROR;
159        painCave.isFatal = 1;
160        simError();
161      }
162          
163      corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
164 +  } else if (args_info.lcorrZ_given) {
165 +    int order;
166 +    if (args_info.order_given)
167 +        order = args_info.order_arg;
168 +    else {
169 +      sprintf( painCave.errMsg,
170 +               "--order must be set if --lcorrZ is set\n");
171 +      painCave.severity = OPENMD_ERROR;
172 +      painCave.isFatal = 1;
173 +      simError();
174 +    }
175 +        
176 +    corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
177 +
178 +  } else if (args_info.cohZ_given) {
179 +    int order;
180 +    if (args_info.order_given)
181 +        order = args_info.order_arg;
182 +    else {
183 +      sprintf( painCave.errMsg,
184 +               "--order must be set if --cohZ is set\n");
185 +      painCave.severity = OPENMD_ERROR;
186 +      painCave.isFatal = 1;
187 +      simError();
188 +    }
189 +        
190 +    corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
191 +
192    }
193  
194 +
195    if (args_info.output_given) {
196      corrFunc->setOutputName(args_info.output_arg);
197    }

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