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root/group/trunk/OOPSE-4/src/applications/staticProps/StaticProps.cpp
Revision: 3223
Committed: Mon Sep 17 20:05:51 2007 UTC (17 years, 7 months ago) by chuckv
File size: 10819 byte(s)
Log Message:
Added code to compute bond angle distributions.

File Contents

# User Rev Content
1 gezelter 2204 /*
2 tim 1994 * 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. 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
19     * notice, this list of conditions and the following disclaimer.
20     *
21     * 3. Redistributions in binary form must reproduce the above copyright
22     * notice, this list of conditions and the following disclaimer in the
23     * documentation and/or other materials provided with the
24     * distribution.
25     *
26     * This software is provided "AS IS," without a warranty of any
27     * kind. All express or implied conditions, representations and
28     * warranties, including any implied warranty of merchantability,
29     * fitness for a particular purpose or non-infringement, are hereby
30     * excluded. The University of Notre Dame and its licensors shall not
31     * be liable for any damages suffered by licensee as a result of
32     * using, modifying or distributing the software or its
33     * derivatives. In no event will the University of Notre Dame or its
34     * licensors be liable for any lost revenue, profit or data, or for
35     * direct, indirect, special, consequential, incidental or punitive
36     * damages, however caused and regardless of the theory of liability,
37     * arising out of the use of or inability to use software, even if the
38     * University of Notre Dame has been advised of the possibility of
39     * such damages.
40     */
41    
42     #include <iostream>
43     #include <fstream>
44     #include <string>
45    
46     #include "brains/Register.hpp"
47     #include "brains/SimCreator.hpp"
48     #include "brains/SimInfo.hpp"
49     #include "io/DumpReader.hpp"
50     #include "utils/simError.h"
51    
52 tim 1995 #include "applications/staticProps/StaticPropsCmd.h"
53 tim 2240 #include "applications/staticProps/StaticAnalyser.hpp"
54 tim 1995 #include "applications/staticProps/GofR.hpp"
55     #include "applications/staticProps/GofRAngle.hpp"
56     #include "applications/staticProps/GofAngle2.hpp"
57     #include "applications/staticProps/GofXyz.hpp"
58 tim 2240 #include "applications/staticProps/P2OrderParameter.hpp"
59 gezelter 3007 #include "applications/staticProps/BondOrderParameter.hpp"
60 chuckv 3128 #include "applications/staticProps/BOPofR.hpp"
61 xsun 2783 #include "applications/staticProps/RippleOP.hpp"
62 tim 2241 #include "applications/staticProps/SCDOrderParameter.hpp"
63 tim 2242 #include "applications/staticProps/DensityPlot.hpp"
64 tim 2539 #include "applications/staticProps/RhoZ.hpp"
65 chuckv 3223 #include "applications/staticProps/BondAngleDistribution.hpp"
66     #include "applications/staticProps/NanoVolume.hpp"
67 gezelter 2753 #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
68 xsun 2751 #include "applications/staticProps/Hxy.hpp"
69 gezelter 2752 #endif
70 chuckv 3076 #include "applications/staticProps/RhoR.hpp"
71 tim 1995
72 tim 1994 using namespace oopse;
73    
74     int main(int argc, char* argv[]){
75    
76 gezelter 2204 //register force fields
77     registerForceFields();
78 tim 1994
79 gezelter 2204 gengetopt_args_info args_info;
80 tim 1994
81 gezelter 2204 //parse the command line option
82     if (cmdline_parser (argc, argv, &args_info) != 0) {
83     exit(1) ;
84     }
85 tim 1994
86 gezelter 3007 //get the dumpfile name
87 gezelter 2204 std::string dumpFileName = args_info.input_arg;
88     std::string sele1;
89     std::string sele2;
90 gezelter 3007 bool userSpecifiedSelect1;
91     bool userSpecifiedSelect2;
92 tim 1994
93 gezelter 3007 // check the first selection argument, or set it to the environment
94     // variable, or failing that, set it to "select all"
95    
96 gezelter 2204 if (args_info.sele1_given) {
97     sele1 = args_info.sele1_arg;
98 gezelter 3007 } else {
99 gezelter 2204 char* sele1Env= getenv("OOPSE_SELE1");
100     if (sele1Env) {
101     sele1 = sele1Env;
102 gezelter 3007 } else {
103     sele1 = "select all";
104 tim 1994 }
105 gezelter 2204 }
106 gezelter 3007
107     // check the second selection argument, or set it to the environment
108     // variable, or failing that, set it to "select all"
109    
110 gezelter 2204 if (args_info.sele2_given) {
111     sele2 = args_info.sele2_arg;
112 gezelter 3007 } else {
113 gezelter 2204 char* sele2Env = getenv("OOPSE_SELE2");
114     if (sele2Env) {
115     sele2 = sele2Env;
116 gezelter 3007 } else {
117 tim 2257 sele2 = "select all";
118 tim 1995 }
119 gezelter 2204 }
120 tim 1994
121 gezelter 3007
122     // Problems if sele1 wasn't specified, but
123     // if (!args_info.scd_given) {
124     // sprintf( painCave.errMsg,
125     // "neither --sele1 option nor $OOPSE_SELE1 is set");
126     // painCave.severity = OOPSE_ERROR;
127     // painCave.isFatal = 1;
128     // simError();
129     // }
130     // }
131    
132     // Problems if sele1 wasn't specified
133    
134     // if(!args_info.scd_given && !args_info.density_given && !args_info.slab_density_given) {
135     // sprintf( painCave.errMsg,
136     // "neither --sele2 option nor $OOPSE_SELE2 is set");
137     // painCave.severity = OOPSE_ERROR;
138     // painCave.isFatal = 1;
139     // simError();
140     // }
141     // }
142    
143 tim 2241 bool batchMode;
144     if (args_info.scd_given){
145     if (args_info.sele1_given && args_info.sele2_given && args_info.sele3_given) {
146 gezelter 3007 batchMode = false;
147 tim 2241 } else if (args_info.molname_given && args_info.begin_given && args_info.end_given) {
148 gezelter 3007 if (args_info.begin_arg < 0 || args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
149 tim 2241 sprintf( painCave.errMsg,
150 gezelter 3007 "below conditions are not satisfied:\n"
151     "0 <= begin && 0<= end && begin <= end-2\n");
152 tim 2241 painCave.severity = OOPSE_ERROR;
153     painCave.isFatal = 1;
154 gezelter 3007 simError();
155     }
156     batchMode = true;
157     } else{
158     sprintf( painCave.errMsg,
159     "either --sele1, --sele2, --sele3 are specified,"
160     " or --molname, --begin, --end are specified\n");
161     painCave.severity = OOPSE_ERROR;
162     painCave.isFatal = 1;
163     simError();
164 tim 2241
165     }
166     }
167    
168 gezelter 2204 //parse md file and set up the system
169     SimCreator creator;
170 gezelter 3021 std::cout << "dumpFile = " << dumpFileName << "\n";
171 gezelter 2984 SimInfo* info = creator.createSim(dumpFileName);
172 tim 1995
173 tim 2759 RealType maxLen;
174 gezelter 2204 if (args_info.length_given) {
175     maxLen = args_info.length_arg;
176     } else {
177     Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
178     maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
179     }
180    
181 tim 2240 StaticAnalyser* analyser;
182 gezelter 2204 if (args_info.gofr_given){
183 gezelter 3009 analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
184     args_info.nbins_arg);
185 gezelter 2204 } else if (args_info.r_theta_given) {
186 gezelter 3009 analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
187     args_info.nbins_arg, args_info.nanglebins_arg);
188 gezelter 2204 } else if (args_info.r_omega_given) {
189 gezelter 3009 analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
190     args_info.nbins_arg, args_info.nanglebins_arg);
191 gezelter 2204 } else if (args_info.theta_omega_given) {
192 gezelter 3009 analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
193     args_info.nanglebins_arg);
194 gezelter 2204 } else if (args_info.gxyz_given) {
195     if (args_info.refsele_given) {
196 gezelter 3009 analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg,
197     maxLen, args_info.nbins_arg);
198 tim 1995 } else {
199 gezelter 2204 sprintf( painCave.errMsg,
200 tim 2053 "--refsele must set when --gxyz is used");
201 gezelter 2204 painCave.severity = OOPSE_ERROR;
202     painCave.isFatal = 1;
203     simError();
204 tim 1995 }
205 tim 2240 } else if (args_info.p2_given) {
206 gezelter 3007 analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
207     } else if (args_info.rp2_given){
208     analyser = new RippleOP(info, dumpFileName, sele1, sele2);
209     } else if (args_info.bo_given){
210 gezelter 3022 if (args_info.rcut_given) {
211 gezelter 3007 analyser = new BondOrderParameter(info, dumpFileName, sele1,
212     args_info.rcut_arg,
213 gezelter 3009 args_info.nbins_arg);
214 gezelter 3007 } else {
215     sprintf( painCave.errMsg,
216 gezelter 3022 "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
217 gezelter 3007 painCave.severity = OOPSE_ERROR;
218     painCave.isFatal = 1;
219     simError();
220     }
221 chuckv 3128 } else if (args_info.bor_given){
222     if (args_info.rcut_given) {
223     analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg,
224     args_info.nbins_arg, maxLen);
225     } else {
226     sprintf( painCave.errMsg,
227     "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
228     painCave.severity = OOPSE_ERROR;
229     painCave.isFatal = 1;
230     simError();
231     }
232 chuckv 3223 } else if (args_info.bad_given){
233     if (args_info.rcut_given) {
234     analyser = new BondAngleDistribution(info, dumpFileName, sele1, args_info.rcut_arg,
235     args_info.nbins_arg);
236     } else {
237     sprintf( painCave.errMsg,
238     "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
239     painCave.severity = OOPSE_ERROR;
240     painCave.isFatal = 1;
241     simError();
242     }
243 gezelter 3007 } else if (args_info.scd_given) {
244     if (batchMode) {
245     analyser = new SCDOrderParameter(info, dumpFileName, args_info.molname_arg,
246     args_info.begin_arg, args_info.end_arg);
247     } else{
248     std::string sele3 = args_info.sele3_arg;
249     analyser = new SCDOrderParameter(info, dumpFileName, sele1, sele2, sele3);
250     }
251 tim 2242 }else if (args_info.density_given) {
252 gezelter 3009 analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
253     args_info.nbins_arg);
254 tim 2539 } else if (args_info.slab_density_given) {
255 gezelter 3007 Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
256 gezelter 3009 analyser = new RhoZ(info, dumpFileName, sele1, hmat(2, 2), args_info.nbins_arg);
257 gezelter 2753 #if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
258 xsun 2751 }else if (args_info.hxy_given) {
259 gezelter 3009 analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
260     args_info.nbins_y_arg, args_info.nbins_arg);
261 gezelter 2752 #endif
262 chuckv 3076 }else if (args_info.rho_r_given) {
263     if (args_info.radius_given){
264     analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
265     }else{
266     sprintf( painCave.errMsg,
267     "A particle radius (radius) must be specified when calculating Rho(r)");
268     painCave.severity = OOPSE_ERROR;
269     painCave.isFatal = 1;
270     simError();
271     }
272 chuckv 3223 }else if (args_info.hullvol_given) {
273     analyser = new NanoVolume(info, dumpFileName, sele1);
274 gezelter 2204 }
275 gezelter 3007
276 gezelter 2204 if (args_info.output_given) {
277 tim 2240 analyser->setOutputName(args_info.output_arg);
278 gezelter 2204 }
279     if (args_info.step_given) {
280 tim 2240 analyser->setStep(args_info.step_arg);
281 gezelter 2204 }
282 tim 1995
283 tim 2240 analyser->process();
284 tim 1995
285 tim 2240 delete analyser;
286 gezelter 2204 delete info;
287 tim 1994
288 gezelter 2204 return 0;
289 tim 1994 }
290    

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