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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 1183 by xsun, Tue Oct 2 12:05:25 2007 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
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).                        
40   */
41  
42   #include <iostream>
# Line 55 | Line 55
55   #include "applications/dynamicProps/LegendreCorrFunc.hpp"
56   #include "applications/dynamicProps/RadialRCorrFunc.hpp"
57   #include "applications/dynamicProps/ThetaCorrFunc.hpp"
58 – #include "applications/dynamicProps/ActionCorrFunc.hpp"
58   #include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
59 + #include "applications/dynamicProps/EnergyCorrFunc.hpp"
60  
61  
62 < using namespace oopse;
62 > using namespace OpenMD;
63  
64   int main(int argc, char* argv[]){
65    
# Line 83 | Line 83 | int main(int argc, char* argv[]){
83    if (args_info.sele1_given) {
84      sele1 = args_info.sele1_arg;
85    }else {
86 <    char*  sele1Env= getenv("OOPSE_SELE1");
86 >    char*  sele1Env= getenv("SELECTION1");
87      if (sele1Env) {
88        sele1 = sele1Env;
89      }else {
90        sprintf( painCave.errMsg,
91 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
92 <      painCave.severity = OOPSE_ERROR;
91 >               "neither --sele1 option nor $SELECTION1 is set");
92 >      painCave.severity = OPENMD_ERROR;
93        painCave.isFatal = 1;
94        simError();
95      }
# Line 98 | Line 98 | int main(int argc, char* argv[]){
98    if (args_info.sele2_given) {
99      sele2 = args_info.sele2_arg;
100    }else {
101 <    char* sele2Env = getenv("OOPSE_SELE2");
101 >    char* sele2Env = getenv("SELECTION2");
102      if (sele2Env) {
103        sele2 = sele2Env;            
104      } else {
# Line 120 | Line 120 | int main(int argc, char* argv[]){
120      corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2);
121    } else if (args_info.thetacorr_given) {
122      corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2);
123 –  } else if (args_info.actioncorr_given) {
124 –    corrFunc = new ActionCorrFunc(info, dumpFileName, sele1, sele2);
123    } else if (args_info.drcorr_given) {
124      corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2);
125 <  }
128 <  else if (args_info.vcorr_given) {
125 >  } else if (args_info.vcorr_given) {
126      corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
127 +  } else if (args_info.helfandEcorr_given){
128 +    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2);  
129    } else if (args_info.lcorr_given) {
130      int order;
131      if (args_info.order_given)
# Line 134 | Line 133 | int main(int argc, char* argv[]){
133      else {
134        sprintf( painCave.errMsg,
135                 "--order must be set if --lcoor is set\n");
136 <      painCave.severity = OOPSE_ERROR;
136 >      painCave.severity = OPENMD_ERROR;
137        painCave.isFatal = 1;
138        simError();
139      }

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