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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 1565 by chuckv, Thu May 19 14:28:04 2011 UTC vs.
Revision 1811 by gezelter, Fri Nov 16 15:12:21 2012 UTC

# Line 36 | Line 36
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).                        
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"
# Line 58 | Line 60
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  
62 –
66   using namespace OpenMD;
67  
68   int main(int argc, char* argv[]){
69    
67 –  //register force fields
68 –  registerForceFields();
69 –
70    gengetopt_args_info args_info;
71  
72    //parse the command line option
# Line 98 | Line 98 | int main(int argc, char* argv[]){
98      
99    if (args_info.sele2_given) {
100      sele2 = args_info.sele2_arg;
101 <  }else {
101 >  } else {
102      char* sele2Env = getenv("SELECTION2");
103      if (sele2Env) {
104        sele2 = sele2Env;            
# Line 107 | Line 107 | int main(int argc, char* argv[]){
107      }
108    }
109  
110 +  // use the memory string to figure out how much memory we can use:
111 +  char *end;
112 +  long long int memSize = memparse(args_info.memory_arg, &end);
113 +  sprintf( painCave.errMsg,
114 +           "Amount of memory being used: %llu bytes\n", memSize);
115 +  painCave.severity = OPENMD_INFO;
116 +  painCave.isFatal = 0;
117 +  simError();    
118 +
119    //parse md file and set up the system
120    SimCreator creator;
121    SimInfo* info = creator.createSim(dumpFileName, false);
122  
114 –
123    TimeCorrFunc* corrFunc;
124 <  if (args_info.dcorr_given){
125 <    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
124 >  if(args_info.sdcorr_given){
125 >    corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
126 >  } else if (args_info.selecorr_given){
127 >    corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
128 >  } else if (args_info.dcorr_given){
129 >    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
130    } else if (args_info.rcorr_given) {
131 <    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
131 >    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132    } else if (args_info.r_rcorr_given) {
133 <    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
133 >    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134    } else if (args_info.thetacorr_given) {
135 <    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
135 >    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136    } else if (args_info.drcorr_given) {
137 <    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
137 >    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
138    } else if (args_info.vcorr_given) {
139 <    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
139 >    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
140    } else if (args_info.helfandEcorr_given){
141 <    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2);
142 <  } else if (args_info.StresCorrFunc_given){
143 <    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2);
141 >    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
142 >  } else if (args_info.stresscorr_given){
143 >    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
144 >  } else if (args_info.momentum_given){
145 >    corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
146    } else if (args_info.lcorr_given) {
147      int order;
148      if (args_info.order_given)
# Line 141 | Line 155 | int main(int argc, char* argv[]){
155        simError();
156      }
157          
158 <    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
158 >    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
159    }
160  
161    if (args_info.output_given) {

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