ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/applications/dynamicProps/DynamicProps.cpp
(Generate patch)

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (file contents):
Revision 876 by tim, Mon Jan 30 22:25:27 2006 UTC vs.
Revision 1596 by gezelter, Mon Jul 25 17:30:53 2011 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 46 | Line 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"
# Line 53 | Line 54
54   #include "applications/dynamicProps/RCorrFunc.hpp"
55   #include "applications/dynamicProps/VCorrFunc.hpp"
56   #include "applications/dynamicProps/LegendreCorrFunc.hpp"
57 + #include "applications/dynamicProps/RadialRCorrFunc.hpp"
58 + #include "applications/dynamicProps/ThetaCorrFunc.hpp"
59 + #include "applications/dynamicProps/DirectionalRCorrFunc.hpp"
60 + #include "applications/dynamicProps/EnergyCorrFunc.hpp"
61 + #include "applications/dynamicProps/StressCorrFunc.hpp"
62  
63  
64 < using namespace oopse;
64 > using namespace OpenMD;
65  
66   int main(int argc, char* argv[]){
67    
# Line 72 | Line 78 | int main(int argc, char* argv[]){
78  
79    //get the dumpfile name and meta-data file name
80    std::string dumpFileName = args_info.input_arg;
75 –
76 –  std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md";
77 –
81      
82    std::string sele1;
83    std::string sele2;
# Line 82 | Line 85 | int main(int argc, char* argv[]){
85    if (args_info.sele1_given) {
86      sele1 = args_info.sele1_arg;
87    }else {
88 <    char*  sele1Env= getenv("OOPSE_SELE1");
88 >    char*  sele1Env= getenv("SELECTION1");
89      if (sele1Env) {
90        sele1 = sele1Env;
91      }else {
92        sprintf( painCave.errMsg,
93 <               "neither --sele1 option nor $OOPSE_SELE1 is set");
94 <      painCave.severity = OOPSE_ERROR;
93 >               "neither --sele1 option nor $SELECTION1 is set");
94 >      painCave.severity = OPENMD_ERROR;
95        painCave.isFatal = 1;
96        simError();
97      }
# Line 97 | Line 100 | int main(int argc, char* argv[]){
100    if (args_info.sele2_given) {
101      sele2 = args_info.sele2_arg;
102    }else {
103 <    char* sele2Env = getenv("OOPSE_SELE2");
103 >    char* sele2Env = getenv("SELECTION2");
104      if (sele2Env) {
105        sele2 = sele2Env;            
106      } else {
# Line 105 | Line 108 | int main(int argc, char* argv[]){
108      }
109    }
110  
111 +  // use the memory string to figure out how much memory we can use:
112 +  char *end;
113 +  long long int memSize = memparse(args_info.memory_arg, &end);
114 +  sprintf( painCave.errMsg,
115 +           "Amount of memory being used: %llu bytes\n", memSize);
116 +  painCave.severity = OPENMD_INFO;
117 +  painCave.isFatal = 0;
118 +  simError();
119 +    
120    //parse md file and set up the system
121    SimCreator creator;
122 <  SimInfo* info = creator.createSim(mdFileName, false);
122 >  SimInfo* info = creator.createSim(dumpFileName, false);
123  
124  
125    TimeCorrFunc* corrFunc;
126    if (args_info.dcorr_given){
127 <    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2);
127 >    corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
128    } else if (args_info.rcorr_given) {
129 <    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2);
130 <  }
131 <  else if (args_info.vcorr_given) {
132 <    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2);
129 >    corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
130 >  } else if (args_info.r_rcorr_given) {
131 >    corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
132 >  } else if (args_info.thetacorr_given) {
133 >    corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
134 >  } else if (args_info.drcorr_given) {
135 >    corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
136 >  } else if (args_info.vcorr_given) {
137 >    corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
138 >  } else if (args_info.helfandEcorr_given){
139 >    corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
140 >  } else if (args_info.stresscorr_given){
141 >    corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
142    } else if (args_info.lcorr_given) {
143      int order;
144      if (args_info.order_given)
# Line 125 | Line 146 | int main(int argc, char* argv[]){
146      else {
147        sprintf( painCave.errMsg,
148                 "--order must be set if --lcoor is set\n");
149 <      painCave.severity = OOPSE_ERROR;
149 >      painCave.severity = OPENMD_ERROR;
150        painCave.isFatal = 1;
151        simError();
152      }
153          
154 <    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order);
154 >    corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
155    }
156  
157    if (args_info.output_given) {

Comparing trunk/src/applications/dynamicProps/DynamicProps.cpp (property svn:keywords):
Revision 876 by tim, Mon Jan 30 22:25:27 2006 UTC vs.
Revision 1596 by gezelter, Mon Jul 25 17:30:53 2011 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines