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root/OpenMD/trunk/src/applications/dynamicProps/DynamicProps.cpp
Revision: 1915
Committed: Mon Jul 29 17:55:17 2013 UTC (11 years, 9 months ago) by gezelter
File size: 6897 byte(s)
Log Message:
Added Legendre Correlation function (as a function of Z), working on architecture for Ewald
Fixed some bugs in FlucQ


File Contents

# Content
1 /*
2 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 *
4 * The University of Notre Dame grants you ("Licensee") a
5 * non-exclusive, royalty free, license to use, modify and
6 * redistribute this software in source and binary code form, provided
7 * that the following conditions are met:
8 *
9 * 1. Redistributions of source code must retain the above copyright
10 * notice, this list of conditions and the following disclaimer.
11 *
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.
16 *
17 * This software is provided "AS IS," without a warranty of any
18 * kind. All express or implied conditions, representations and
19 * warranties, including any implied warranty of merchantability,
20 * fitness for a particular purpose or non-infringement, are hereby
21 * excluded. The University of Notre Dame and its licensors shall not
22 * be liable for any damages suffered by licensee as a result of
23 * using, modifying or distributing the software or its
24 * derivatives. In no event will the University of Notre Dame or its
25 * licensors be liable for any lost revenue, profit or data, or for
26 * direct, indirect, special, consequential, incidental or punitive
27 * damages, however caused and regardless of the theory of liability,
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, 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
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
67 using namespace OpenMD;
68
69 int main(int argc, char* argv[]){
70
71 gengetopt_args_info args_info;
72
73 //parse the command line option
74 if (cmdline_parser (argc, argv, &args_info) != 0) {
75 exit(1) ;
76 }
77
78
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
85 if (args_info.sele1_given) {
86 sele1 = args_info.sele1_arg;
87 }else {
88 char* sele1Env= getenv("SELECTION1");
89 if (sele1Env) {
90 sele1 = sele1Env;
91 }else {
92 sprintf( painCave.errMsg,
93 "neither --sele1 option nor $SELECTION1 is set");
94 painCave.severity = OPENMD_ERROR;
95 painCave.isFatal = 1;
96 simError();
97 }
98 }
99
100 if (args_info.sele2_given) {
101 sele2 = args_info.sele2_arg;
102 } else {
103 char* sele2Env = getenv("SELECTION2");
104 if (sele2Env) {
105 sele2 = sele2Env;
106 } else {
107 sele2 = sele1;
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(dumpFileName, false);
123
124 TimeCorrFunc* corrFunc;
125 if(args_info.sdcorr_given){
126 corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
127 } else if (args_info.selecorr_given){
128 corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize);
129 } else if (args_info.dcorr_given){
130 corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize);
131 } else if (args_info.rcorr_given) {
132 corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize);
133 } else if (args_info.r_rcorr_given) {
134 corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
135 } else if (args_info.thetacorr_given) {
136 corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize);
137 } else if (args_info.drcorr_given) {
138 corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize);
139 } else if (args_info.vcorr_given) {
140 corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize);
141 } else if (args_info.helfandEcorr_given){
142 corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize);
143 } else if (args_info.stresscorr_given){
144 corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize);
145 } else if (args_info.momentum_given){
146 corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize);
147 } else if (args_info.lcorr_given) {
148 int order;
149 if (args_info.order_given)
150 order = args_info.order_arg;
151 else {
152 sprintf( painCave.errMsg,
153 "--order must be set if --lcorr is set\n");
154 painCave.severity = OPENMD_ERROR;
155 painCave.isFatal = 1;
156 simError();
157 }
158
159 corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize);
160 } else if (args_info.lcorrZ_given) {
161 int order;
162 if (args_info.order_given)
163 order = args_info.order_arg;
164 else {
165 sprintf( painCave.errMsg,
166 "--order must be set if --lcorrZ is set\n");
167 painCave.severity = OPENMD_ERROR;
168 painCave.isFatal = 1;
169 simError();
170 }
171
172 corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize);
173
174 }
175
176 if (args_info.output_given) {
177 corrFunc->setOutputName(args_info.output_arg);
178 }
179
180
181 corrFunc->doCorrelate();
182
183 delete corrFunc;
184 delete info;
185
186 return 0;
187 }
188
189

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