applications/sequentialProps/SequentialProps.cpp

/*
 * Copyright (c) 2014 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include <iostream>
#include <fstream>
#include <string>

#include "brains/SimCreator.hpp"
#include "brains/SimInfo.hpp"
#include "utils/StringUtils.hpp"
#include "utils/simError.h"

#include "applications/sequentialProps/SequentialPropsCmd.h"
#include "applications/sequentialProps/SequentialAnalyzer.hpp"
#include "applications/sequentialProps/CenterOfMass.hpp"
#include "applications/sequentialProps/ContactAngle1.hpp"
#include "applications/sequentialProps/ContactAngle2.hpp"

using namespace OpenMD;

int main(int argc, char* argv[]){
  
  gengetopt_args_info args_info;

  //parse the command line option
  if (cmdline_parser (argc, argv, &args_info) != 0) {
    exit(1) ;
  }

  //get the dumpfile name and meta-data file name
  std::string dumpFileName = args_info.input_arg;
    
  std::string sele1;
  std::string sele2;
  
  // check the first selection argument, or set it to the environment
  // variable, or failing that, set it to "select all"
  
  if (args_info.sele1_given) {
    sele1 = args_info.sele1_arg;
  } else {
    char*  sele1Env= getenv("SELECTION1");
    if (sele1Env) {
      sele1 = sele1Env;
    } else {
      sele1 = "select all";
    }
  }
  
  // check the second selection argument, or set it to the environment
  // variable, or failing that, set it to the first selection
  
  if (args_info.sele2_given) {
    sele2 = args_info.sele2_arg;
  } else {
    char* sele2Env = getenv("SELECTION2");
    if (sele2Env) {
      sele2 = sele2Env;            
    } else { 
      //If sele2 is not specified, then the default behavior
      //should be what is already intended for sele1
      sele2 = sele1;
    }
  }

  //parse md file and set up the system
  SimCreator creator;
  SimInfo* info = creator.createSim(dumpFileName, false);

  SequentialAnalyzer* analyzer;
  if(args_info.com_given){
    analyzer = new CenterOfMass(info, dumpFileName, sele1);
  } else if(args_info.ca1_given){
    RealType solidZ;
    if (args_info.referenceZ_given)
        solidZ = args_info.referenceZ_arg;
    else {
      sprintf( painCave.errMsg,
               "--referenceZ must be set if --ca1 is used\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    RealType dropletR;
    if (args_info.dropletR_given)
        dropletR = args_info.dropletR_arg;
    else {
      sprintf( painCave.errMsg,
               "--dropletR must be set if --ca1 is used\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }

    analyzer = new ContactAngle1(info, dumpFileName, sele1, solidZ, dropletR);
  } else if(args_info.ca2_given){
    RealType solidZ;
    if (args_info.referenceZ_given)
        solidZ = args_info.referenceZ_arg;
    else {
      sprintf( painCave.errMsg,
               "--referenceZ must be set if --ca2 is used\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    RealType threshDens;
    if (args_info.threshDens_given)
        threshDens = args_info.threshDens_arg;
    else {
      sprintf( painCave.errMsg,
               "--threshDens must be set if --ca1 is used\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }

    analyzer = new ContactAngle2(info, dumpFileName, sele1, solidZ,
                                 threshDens, args_info.nbins_arg,
                                 args_info.nbins_z_arg);
  }

  if (args_info.output_given) {
    analyzer->setOutputName(args_info.output_arg);
  }

  analyzer->doSequence();

  delete analyzer;    
  delete info;

  return 0;   
}


Revision:	2035
Committed:	Tue Nov 4 15:31:51 2014 UTC (10 years, 5 months ago) by gezelter
File size:	5788 byte(s)
Log Message:	First checkin of the second contact angle method for sequentialProps.
#	User	Rev	Content
1	gezelter	2024	/*
2			* Copyright (c) 2014 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/sequentialProps/SequentialPropsCmd.h"
53			#include "applications/sequentialProps/SequentialAnalyzer.hpp"
54	gezelter	2029	#include "applications/sequentialProps/CenterOfMass.hpp"
55			#include "applications/sequentialProps/ContactAngle1.hpp"
56	gezelter	2035	#include "applications/sequentialProps/ContactAngle2.hpp"
57	gezelter	2024
58			using namespace OpenMD;
59
60			int main(int argc, char* argv[]){
61
62			gengetopt_args_info args_info;
63
64			//parse the command line option
65			if (cmdline_parser (argc, argv, &args_info) != 0) {
66			exit(1) ;
67			}
68
69			//get the dumpfile name and meta-data file name
70			std::string dumpFileName = args_info.input_arg;
71
72			std::string sele1;
73			std::string sele2;
74
75			// check the first selection argument, or set it to the environment
76			// variable, or failing that, set it to "select all"
77
78			if (args_info.sele1_given) {
79			sele1 = args_info.sele1_arg;
80			} else {
81			char* sele1Env= getenv("SELECTION1");
82			if (sele1Env) {
83			sele1 = sele1Env;
84			} else {
85			sele1 = "select all";
86			}
87			}
88
89			// check the second selection argument, or set it to the environment
90			// variable, or failing that, set it to the first selection
91
92			if (args_info.sele2_given) {
93			sele2 = args_info.sele2_arg;
94			} else {
95			char* sele2Env = getenv("SELECTION2");
96			if (sele2Env) {
97			sele2 = sele2Env;
98			} else {
99			//If sele2 is not specified, then the default behavior
100			//should be what is already intended for sele1
101			sele2 = sele1;
102			}
103			}
104
105			//parse md file and set up the system
106			SimCreator creator;
107			SimInfo* info = creator.createSim(dumpFileName, false);
108
109			SequentialAnalyzer* analyzer;
110	gezelter	2029	if(args_info.com_given){
111			analyzer = new CenterOfMass(info, dumpFileName, sele1);
112			} else if(args_info.ca1_given){
113			RealType solidZ;
114			if (args_info.referenceZ_given)
115			solidZ = args_info.referenceZ_arg;
116			else {
117			sprintf( painCave.errMsg,
118			"--referenceZ must be set if --ca1 is used\n");
119			painCave.severity = OPENMD_ERROR;
120			painCave.isFatal = 1;
121			simError();
122			}
123			RealType dropletR;
124			if (args_info.dropletR_given)
125			dropletR = args_info.dropletR_arg;
126			else {
127			sprintf( painCave.errMsg,
128			"--dropletR must be set if --ca1 is used\n");
129			painCave.severity = OPENMD_ERROR;
130			painCave.isFatal = 1;
131			simError();
132			}
133
134			analyzer = new ContactAngle1(info, dumpFileName, sele1, solidZ, dropletR);
135	gezelter	2035	} else if(args_info.ca2_given){
136			RealType solidZ;
137			if (args_info.referenceZ_given)
138			solidZ = args_info.referenceZ_arg;
139			else {
140			sprintf( painCave.errMsg,
141			"--referenceZ must be set if --ca2 is used\n");
142			painCave.severity = OPENMD_ERROR;
143			painCave.isFatal = 1;
144			simError();
145			}
146			RealType threshDens;
147			if (args_info.threshDens_given)
148			threshDens = args_info.threshDens_arg;
149			else {
150			sprintf( painCave.errMsg,
151			"--threshDens must be set if --ca1 is used\n");
152			painCave.severity = OPENMD_ERROR;
153			painCave.isFatal = 1;
154			simError();
155			}
156
157			analyzer = new ContactAngle2(info, dumpFileName, sele1, solidZ,
158			threshDens, args_info.nbins_arg,
159			args_info.nbins_z_arg);
160	gezelter	2024	}
161
162			if (args_info.output_given) {
163			analyzer->setOutputName(args_info.output_arg);
164			}
165
166			analyzer->doSequence();
167
168			delete analyzer;
169			delete info;
170
171			return 0;
172			}
173
174