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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 1566 by chuckv, Thu May 19 18:12:09 2011 UTC vs.
Revision 2003 by gezelter, Sun Jun 1 19:28:44 2014 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 + #include "applications/dynamicProps/FreqFlucCorrFunc.hpp"
69  
62 –
70   using namespace OpenMD;
71  
72   int main(int argc, char* argv[]){
73    
67 –  //register force fields
68 –  registerForceFields();
69 –
74    gengetopt_args_info args_info;
75  
76    //parse the command line option
# Line 74 | Line 78 | int main(int argc, char* argv[]){
78      exit(1) ;
79    }
80  
77 –
81    //get the dumpfile name and meta-data file name
82    std::string dumpFileName = args_info.input_arg;
83      
84    std::string sele1;
85    std::string sele2;
86 <
86 >  
87 >  // check the first selection argument, or set it to the environment
88 >  // variable, or failing that, set it to "select all"
89 >  
90    if (args_info.sele1_given) {
91      sele1 = args_info.sele1_arg;
92 <  }else {
92 >  } else {
93      char*  sele1Env= getenv("SELECTION1");
94      if (sele1Env) {
95        sele1 = sele1Env;
96 <    }else {
97 <      sprintf( painCave.errMsg,
92 <               "neither --sele1 option nor $SELECTION1 is set");
93 <      painCave.severity = OPENMD_ERROR;
94 <      painCave.isFatal = 1;
95 <      simError();
96 >    } else {
97 >      sele1 = "select all";
98      }
99    }
100 <    
100 >  
101 >  // check the second selection argument, or set it to the environment
102 >  // variable, or failing that, set it to the first selection
103 >  
104    if (args_info.sele2_given) {
105      sele2 = args_info.sele2_arg;
106 <  }else {
106 >  } else {
107      char* sele2Env = getenv("SELECTION2");
108      if (sele2Env) {
109        sele2 = sele2Env;            
110 <    } else {
110 >    } else {
111 >      //If sele2 is not specified, then the default behavior
112 >      //should be what is already intended for sele1
113        sele2 = sele1;
114      }
115    }
116  
117 +  // use the memory string to figure out how much memory we can use:
118 +  char *end;
119 +  long long int memSize = memparse(args_info.memory_arg, &end);
120 +  sprintf( painCave.errMsg,
121 +           "Amount of memory being used: %llu bytes\n", memSize);
122 +  painCave.severity = OPENMD_INFO;
123 +  painCave.isFatal = 0;
124 +  simError();    
125 +
126    //parse md file and set up the system
127    SimCreator creator;
128    SimInfo* info = creator.createSim(dumpFileName, false);
129  
114 –
130    TimeCorrFunc* corrFunc;
131 <  if (args_info.dcorr_given){
132 <    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
131 >  if(args_info.sdcorr_given){
132 >    corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
133 >  } else if (args_info.selecorr_given){
134 >    corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
135 >  } else if (args_info.dcorr_given){
136 >    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
137    } else if (args_info.rcorr_given) {
138 <    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
138 >    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
139    } else if (args_info.r_rcorr_given) {
140 <    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
140 >    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
141    } else if (args_info.thetacorr_given) {
142 <    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
142 >    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
143    } else if (args_info.drcorr_given) {
144 <    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
144 >    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
145    } else if (args_info.vcorr_given) {
146 <    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
146 >    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
147 >  } else if (args_info.bondcorr_given) {
148 >    corrFunc = new BondCorrFunc(info, dumpFileName, sele1, memSize);
149    } else if (args_info.helfandEcorr_given){
150 <    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2);
150 >    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
151    } else if (args_info.stresscorr_given){
152 <    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2);
152 >    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
153 >  } else if (args_info.momentum_given){
154 >    corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
155 >  } else if (args_info.freqfluccorr_given){
156 >    corrFunc = new FreqFlucCorrFunc(info, dumpFileName, sele1, sele2, memSize);
157    } else if (args_info.lcorr_given) {
158      int order;
159      if (args_info.order_given)
160          order = args_info.order_arg;
161      else {
162        sprintf( painCave.errMsg,
163 <               "--order must be set if --lcoor is set\n");
163 >               "--order must be set if --lcorr is set\n");
164        painCave.severity = OPENMD_ERROR;
165        painCave.isFatal = 1;
166        simError();
167      }
168          
169 <    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
169 >    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
170 >  } else if (args_info.lcorrZ_given) {
171 >    int order;
172 >    if (args_info.order_given)
173 >        order = args_info.order_arg;
174 >    else {
175 >      sprintf( painCave.errMsg,
176 >               "--order must be set if --lcorrZ is set\n");
177 >      painCave.severity = OPENMD_ERROR;
178 >      painCave.isFatal = 1;
179 >      simError();
180 >    }
181 >        
182 >    corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
183 >
184 >  } else if (args_info.cohZ_given) {
185 >    int order;
186 >    if (args_info.order_given)
187 >        order = args_info.order_arg;
188 >    else {
189 >      sprintf( painCave.errMsg,
190 >               "--order must be set if --cohZ is set\n");
191 >      painCave.severity = OPENMD_ERROR;
192 >      painCave.isFatal = 1;
193 >      simError();
194 >    }
195 >        
196 >    corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
197 >
198    }
199  
200 +
201    if (args_info.output_given) {
202      corrFunc->setOutputName(args_info.output_arg);
203    }

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