applications/staticProps/StaticProps.cpp

/*
 * Copyright (c) 2005 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 "io/DumpReader.hpp"
#include "utils/simError.h"

#include "applications/staticProps/StaticPropsCmd.h"
#include "applications/staticProps/StaticAnalyser.hpp"
#include "applications/staticProps/GofR.hpp"
#include "applications/staticProps/GofZ.hpp"
#include "applications/staticProps/GofRZ.hpp"
#include "applications/staticProps/GofRAngle.hpp"
#include "applications/staticProps/GofAngle2.hpp"
#include "applications/staticProps/GofXyz.hpp"
#include "applications/staticProps/TwoDGofR.hpp"
#include "applications/staticProps/P2OrderParameter.hpp"
#include "applications/staticProps/BondOrderParameter.hpp"
#include "applications/staticProps/BOPofR.hpp"
#include "applications/staticProps/RippleOP.hpp"
#include "applications/staticProps/SCDOrderParameter.hpp"
#include "applications/staticProps/DensityPlot.hpp"
#include "applications/staticProps/ObjectCount.hpp"
#include "applications/staticProps/RhoZ.hpp"
#include "applications/staticProps/pAngle.hpp"
#include "applications/staticProps/BondAngleDistribution.hpp"
#include "applications/staticProps/NanoVolume.hpp"
#include "applications/staticProps/NanoLength.hpp"
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
#include "applications/staticProps/Hxy.hpp"
#endif
#include "applications/staticProps/RhoR.hpp"
#include "applications/staticProps/AngleR.hpp"
#include "applications/staticProps/TetrahedralityParam.hpp"
#include "applications/staticProps/TetrahedralityParamZ.hpp"
#include "applications/staticProps/TetrahedralityParamXYZ.hpp"
#include "applications/staticProps/RNEMDStats.hpp"
#include "applications/staticProps/NitrileFrequencyMap.hpp"
#include "applications/staticProps/MultipoleSum.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
  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;
    }
  }

  bool batchMode;
  if (args_info.scd_given){
    if (args_info.sele1_given && 
        args_info.sele2_given && args_info.sele3_given) {
      batchMode = false;
    } else if (args_info.molname_given && 
               args_info.begin_given && args_info.end_given) {
      if (args_info.begin_arg < 0 || 
          args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) {
        sprintf( painCave.errMsg,
                 "below conditions are not satisfied:\n"
                 "0 <= begin && 0<= end && begin <= end-2\n");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();                    
      }
      batchMode = true;        
    } else{
      sprintf( painCave.errMsg,
               "either --sele1, --sele2, --sele3 are specified,"
               " or --molname, --begin, --end are specified\n");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  }
  
  //parse md file and set up the system
  SimCreator creator;
  SimInfo* info = creator.createSim(dumpFileName);

  RealType maxLen;
  RealType zmaxLen;
  if (args_info.length_given) {
    maxLen = args_info.length_arg;
    if (args_info.zlength_given){
      zmaxLen = args_info.zlength_arg;
    }
  } else {
    Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
    maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
    zmaxLen = hmat(2,2);    
  }    
  
  StaticAnalyser* analyser;
  if (args_info.gofr_given){
    analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, 
                       args_info.nbins_arg);        
  } else if (args_info.gofz_given) {
    analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
                       args_info.nbins_arg);
  } else if (args_info.r_z_given) {
    analyser  = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen, 
                          args_info.nbins_arg, args_info.nbins_z_arg);
  } else if (args_info.r_theta_given) {
    analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, 
                              args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.r_omega_given) {
    analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, 
                              args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.theta_omega_given) {
    analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, 
                              args_info.nanglebins_arg);
  } else if (args_info.gxyz_given) {
    if (args_info.refsele_given) {
      analyser= new GofXyz(info, dumpFileName, sele1, sele2,
                           args_info.refsele_arg, maxLen, args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "--refsele must set when --gxyz is used");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();  
    }
  } else if (args_info.twodgofr_given){
    if (args_info.dz_given) {
      analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen, 
                             args_info.dz_arg, args_info.nbins_arg);        
    } else {
      sprintf( painCave.errMsg,
               "A slab width (dz) must be specified when calculating TwoDGofR");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }    
  } else if (args_info.p2_given) {
    if (args_info.sele1_given) {     
      if (args_info.sele2_given) 
        analyser  = new P2OrderParameter(info, dumpFileName, sele1, sele2);
      else 
        if (args_info.seleoffset_given) 
          analyser  = new P2OrderParameter(info, dumpFileName, sele1, 
                                           args_info.seleoffset_arg);
        else 
          analyser  = new P2OrderParameter(info, dumpFileName, sele1);
    } else {
      sprintf( painCave.errMsg,
               "At least one selection script (--sele1) must be specified when calculating P2 order parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.rp2_given){
    analyser = new RippleOP(info, dumpFileName, sele1, sele2);
  } else if (args_info.bo_given){
    if (args_info.rcut_given) {
      analyser = new BondOrderParameter(info, dumpFileName, sele1, 
                                        args_info.rcut_arg, 
                                        args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.multipole_given){
    analyser = new MultipoleSum(info, dumpFileName, sele1, 
                                maxLen, args_info.nbins_arg);
  } else if (args_info.tet_param_given) {
    if (args_info.rcut_given) {   
      analyser = new TetrahedralityParam(info, dumpFileName, sele1, 
                                         args_info.rcut_arg, 
                                         args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.tet_param_z_given) {
    if (args_info.rcut_given) {   
      analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
                                          args_info.rcut_arg, 
                                          args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.tet_param_xyz_given) {
    if (!args_info.rcut_given) {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating"
               " Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    if (!args_info.voxelSize_given) {
      sprintf( painCave.errMsg,
               "A voxel size must be specified when calculating"
               " volume-resolved Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    if (!args_info.gaussWidth_given) {
      sprintf( painCave.errMsg,
               "A gaussian width must be specified when calculating"
               " volume-resolved Tetrahedrality Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
    analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
                                          args_info.rcut_arg, 
                                          args_info.voxelSize_arg,
                                          args_info.gaussWidth_arg);
  } else if (args_info.ior_given){
    if (args_info.rcut_given) {
      analyser = new IcosahedralOfR(info, dumpFileName, sele1, 
                                    args_info.rcut_arg,
                                    args_info.nbins_arg, maxLen);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.for_given){
    if (args_info.rcut_given) {
      analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
                            args_info.nbins_arg, maxLen);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.bad_given){
    if (args_info.rcut_given) {
      analyser = new BondAngleDistribution(info, dumpFileName, sele1, 
                                           args_info.rcut_arg,
                                           args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.scd_given) {
    if (batchMode) {
      analyser  = new SCDOrderParameter(info, dumpFileName, 
                                        args_info.molname_arg, 
                                        args_info.begin_arg, args_info.end_arg);
    } else{
      std::string sele3 = args_info.sele3_arg;
      analyser  = new SCDOrderParameter(info, dumpFileName, 
                                        sele1, sele2, sele3);
    }
  }else if (args_info.density_given) {
    analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
                              args_info.nbins_arg);  
  } else if (args_info.count_given) {
    analyser = new ObjectCount(info, dumpFileName, sele1 );
  } else if (args_info.slab_density_given) {
    analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
  } else if (args_info.rnemdz_given) {
    analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
  } else if (args_info.rnemdr_given) {
    analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
  } else if (args_info.rnemdrt_given) {
    analyser = new RNEMDRTheta(info, dumpFileName, sele1,
                               args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.nitrile_given) {
    analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
                                       args_info.nbins_arg);
  } else if (args_info.p_angle_given) {
    if (args_info.sele1_given) {     
      if (args_info.sele2_given) 
        analyser  = new pAngle(info, dumpFileName, sele1, sele2,
                               args_info.nbins_arg);
      else 
        if (args_info.seleoffset_given) {
          if (args_info.seleoffset2_given) {
            analyser  = new pAngle(info, dumpFileName, sele1, 
                                   args_info.seleoffset_arg, 
                                   args_info.seleoffset2_arg, 
                                   args_info.nbins_arg);
          } else {
            analyser  = new pAngle(info, dumpFileName, sele1, 
                                   args_info.seleoffset_arg, 
                                   args_info.nbins_arg);
          }
        } else 
          analyser  = new pAngle(info, dumpFileName, sele1, 
                                 args_info.nbins_arg);
    } else {
      sprintf( painCave.errMsg,
               "At least one selection script (--sele1) must be specified when "
               "calculating P(angle) distributions");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H)
  }else if (args_info.hxy_given) {
    analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, 
                       args_info.nbins_y_arg, args_info.nbins_arg);
#endif
  }else if (args_info.rho_r_given) {
    if (args_info.radius_given){
      analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
    }else{
      sprintf( painCave.errMsg,
               "A particle radius (radius) must be specified when calculating Rho(r)");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }
  } else if (args_info.hullvol_given) {
    analyser = new NanoVolume(info, dumpFileName, sele1);
  } else if (args_info.rodlength_given) {
    analyser = new NanoLength(info, dumpFileName, sele1);
  } else if (args_info.angle_r_given) {
    analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
  }
  
  if (args_info.output_given) {
    analyser->setOutputName(args_info.output_arg);
  }
  if (args_info.step_given) {
    analyser->setStep(args_info.step_arg);
  }
  
  analyser->process();
  
  delete analyser;    
  delete info;
  
  return 0;   
}
Revision:	2015
Committed:	Wed Aug 13 20:42:43 2014 UTC (10 years, 8 months ago) by gezelter
File size:	16965 byte(s)
Log Message:	Changes to include the volume-resolved tetrahedrality parameter.
#	User	Rev	Content
1	gezelter	507	/*
2	tim	310	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	310	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	310	* 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	gezelter	1390	*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	310	*/
42
43			#include <iostream>
44			#include <fstream>
45			#include <string>
46
47			#include "brains/SimCreator.hpp"
48			#include "brains/SimInfo.hpp"
49			#include "io/DumpReader.hpp"
50			#include "utils/simError.h"
51
52	tim	311	#include "applications/staticProps/StaticPropsCmd.h"
53	tim	543	#include "applications/staticProps/StaticAnalyser.hpp"
54	tim	311	#include "applications/staticProps/GofR.hpp"
55	xsun	1213	#include "applications/staticProps/GofZ.hpp"
56	gezelter	1440	#include "applications/staticProps/GofRZ.hpp"
57	tim	311	#include "applications/staticProps/GofRAngle.hpp"
58			#include "applications/staticProps/GofAngle2.hpp"
59			#include "applications/staticProps/GofXyz.hpp"
60	gezelter	1454	#include "applications/staticProps/TwoDGofR.hpp"
61	tim	543	#include "applications/staticProps/P2OrderParameter.hpp"
62	gezelter	1039	#include "applications/staticProps/BondOrderParameter.hpp"
63	chuckv	1128	#include "applications/staticProps/BOPofR.hpp"
64	xsun	980	#include "applications/staticProps/RippleOP.hpp"
65	tim	544	#include "applications/staticProps/SCDOrderParameter.hpp"
66	tim	545	#include "applications/staticProps/DensityPlot.hpp"
67	gezelter	1513	#include "applications/staticProps/ObjectCount.hpp"
68	tim	840	#include "applications/staticProps/RhoZ.hpp"
69	gezelter	1413	#include "applications/staticProps/pAngle.hpp"
70	chuckv	1180	#include "applications/staticProps/BondAngleDistribution.hpp"
71			#include "applications/staticProps/NanoVolume.hpp"
72	gezelter	1585	#include "applications/staticProps/NanoLength.hpp"
73	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
74	xsun	955	#include "applications/staticProps/Hxy.hpp"
75	gezelter	956	#endif
76	chuckv	1091	#include "applications/staticProps/RhoR.hpp"
77	kstocke1	1522	#include "applications/staticProps/AngleR.hpp"
78			#include "applications/staticProps/TetrahedralityParam.hpp"
79	gezelter	1782	#include "applications/staticProps/TetrahedralityParamZ.hpp"
80	gezelter	2015	#include "applications/staticProps/TetrahedralityParamXYZ.hpp"
81	gezelter	1879	#include "applications/staticProps/RNEMDStats.hpp"
82	gezelter	1994	#include "applications/staticProps/NitrileFrequencyMap.hpp"
83	gezelter	1998	#include "applications/staticProps/MultipoleSum.hpp"
84	gezelter	1879
85	gezelter	1390	using namespace OpenMD;
86	tim	310
87			int main(int argc, char* argv[]){
88
89	gezelter	1513
90			gengetopt_args_info args_info;
91
92			//parse the command line option
93			if (cmdline_parser (argc, argv, &args_info) != 0) {
94			exit(1) ;
95			}
96
97			//get the dumpfile name
98			std::string dumpFileName = args_info.input_arg;
99			std::string sele1;
100			std::string sele2;
101
102			// check the first selection argument, or set it to the environment
103			// variable, or failing that, set it to "select all"
104
105			if (args_info.sele1_given) {
106			sele1 = args_info.sele1_arg;
107			} else {
108			char* sele1Env= getenv("SELECTION1");
109			if (sele1Env) {
110			sele1 = sele1Env;
111			} else {
112			sele1 = "select all";
113			}
114			}
115
116			// check the second selection argument, or set it to the environment
117	gezelter	1937	// variable, or failing that, set it to the first selection
118	gezelter	1513
119			if (args_info.sele2_given) {
120			sele2 = args_info.sele2_arg;
121			} else {
122	gezelter	1937	char* sele2Env = getenv("SELECTION2");
123	gezelter	1513	if (sele2Env) {
124			sele2 = sele2Env;
125			} else {
126	gezelter	1819	//If sele2 is not specified, then the default behavior
127			//should be what is already intended for sele1
128	jmichalk	1785	sele2 = sele1;
129	gezelter	1513	}
130			}
131	gezelter	1846
132	gezelter	1513	bool batchMode;
133			if (args_info.scd_given){
134	gezelter	1846	if (args_info.sele1_given &&
135			args_info.sele2_given && args_info.sele3_given) {
136	gezelter	1513	batchMode = false;
137	gezelter	1846	} else if (args_info.molname_given &&
138			args_info.begin_given && args_info.end_given) {
139			if (args_info.begin_arg < 0 \|\|
140			args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
141	gezelter	1513	sprintf( painCave.errMsg,
142			"below conditions are not satisfied:\n"
143			"0 <= begin && 0<= end && begin <= end-2\n");
144			painCave.severity = OPENMD_ERROR;
145			painCave.isFatal = 1;
146			simError();
147			}
148			batchMode = true;
149			} else{
150			sprintf( painCave.errMsg,
151			"either --sele1, --sele2, --sele3 are specified,"
152			" or --molname, --begin, --end are specified\n");
153			painCave.severity = OPENMD_ERROR;
154			painCave.isFatal = 1;
155	gezelter	1846	simError();
156	gezelter	1513	}
157			}
158
159			//parse md file and set up the system
160			SimCreator creator;
161			SimInfo* info = creator.createSim(dumpFileName);
162	tim	310
163	gezelter	1513	RealType maxLen;
164			RealType zmaxLen;
165			if (args_info.length_given) {
166			maxLen = args_info.length_arg;
167			if (args_info.zlength_given){
168			zmaxLen = args_info.zlength_arg;
169	chuckv	1445	}
170	gezelter	1513	} else {
171			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
172			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
173			zmaxLen = hmat(2,2);
174			}
175	kstocke1	1522
176	gezelter	1513	StaticAnalyser* analyser;
177			if (args_info.gofr_given){
178			analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
179	kstocke1	1522	args_info.nbins_arg);
180	gezelter	1513	} else if (args_info.gofz_given) {
181			analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
182	kstocke1	1522	args_info.nbins_arg);
183	gezelter	1513	} else if (args_info.r_z_given) {
184			analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
185	kstocke1	1522	args_info.nbins_arg, args_info.nbins_z_arg);
186	gezelter	1513	} else if (args_info.r_theta_given) {
187			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
188	kstocke1	1522	args_info.nbins_arg, args_info.nanglebins_arg);
189	gezelter	1513	} else if (args_info.r_omega_given) {
190			analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
191	kstocke1	1522	args_info.nbins_arg, args_info.nanglebins_arg);
192	gezelter	1513	} else if (args_info.theta_omega_given) {
193			analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
194	kstocke1	1522	args_info.nanglebins_arg);
195	gezelter	1513	} else if (args_info.gxyz_given) {
196			if (args_info.refsele_given) {
197	gezelter	1846	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
198			args_info.refsele_arg, maxLen, args_info.nbins_arg);
199	gezelter	1039	} else {
200	gezelter	1513	sprintf( painCave.errMsg,
201	kstocke1	1522	"--refsele must set when --gxyz is used");
202	gezelter	1513	painCave.severity = OPENMD_ERROR;
203			painCave.isFatal = 1;
204			simError();
205	tim	310	}
206	gezelter	1513	} else if (args_info.twodgofr_given){
207			if (args_info.dz_given) {
208			analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
209	kstocke1	1522	args_info.dz_arg, args_info.nbins_arg);
210	chuckv	1445	} else {
211	gezelter	1513	sprintf( painCave.errMsg,
212	kstocke1	1522	"A slab width (dz) must be specified when calculating TwoDGofR");
213	gezelter	1513	painCave.severity = OPENMD_ERROR;
214			painCave.isFatal = 1;
215			simError();
216	kstocke1	1522	}
217	gezelter	1513	} else if (args_info.p2_given) {
218	gezelter	1542	if (args_info.sele1_given) {
219			if (args_info.sele2_given)
220			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
221			else
222	gezelter	1819	if (args_info.seleoffset_given)
223			analyser = new P2OrderParameter(info, dumpFileName, sele1,
224			args_info.seleoffset_arg);
225			else
226			analyser = new P2OrderParameter(info, dumpFileName, sele1);
227	gezelter	1542	} else {
228			sprintf( painCave.errMsg,
229			"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
230			painCave.severity = OPENMD_ERROR;
231			painCave.isFatal = 1;
232			simError();
233			}
234	gezelter	1513	} else if (args_info.rp2_given){
235			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
236			} else if (args_info.bo_given){
237			if (args_info.rcut_given) {
238			analyser = new BondOrderParameter(info, dumpFileName, sele1,
239	kstocke1	1522	args_info.rcut_arg,
240			args_info.nbins_arg);
241	gezelter	1513	} else {
242			sprintf( painCave.errMsg,
243	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
244	gezelter	1513	painCave.severity = OPENMD_ERROR;
245			painCave.isFatal = 1;
246			simError();
247	tim	544	}
248	gezelter	1998	} else if (args_info.multipole_given){
249	gezelter	1999	analyser = new MultipoleSum(info, dumpFileName, sele1,
250			maxLen, args_info.nbins_arg);
251	kstocke1	1522	} else if (args_info.tet_param_given) {
252			if (args_info.rcut_given) {
253			analyser = new TetrahedralityParam(info, dumpFileName, sele1,
254			args_info.rcut_arg,
255			args_info.nbins_arg);
256			} else {
257			sprintf( painCave.errMsg,
258			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
259			painCave.severity = OPENMD_ERROR;
260			painCave.isFatal = 1;
261			simError();
262			}
263	gezelter	1782	} else if (args_info.tet_param_z_given) {
264			if (args_info.rcut_given) {
265	gezelter	1846	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
266			args_info.rcut_arg,
267			args_info.nbins_arg);
268	gezelter	1782	} else {
269			sprintf( painCave.errMsg,
270			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
271			painCave.severity = OPENMD_ERROR;
272			painCave.isFatal = 1;
273			simError();
274			}
275	gezelter	2015	} else if (args_info.tet_param_xyz_given) {
276			if (!args_info.rcut_given) {
277			sprintf( painCave.errMsg,
278			"A cutoff radius (rcut) must be specified when calculating"
279			" Tetrahedrality Parameters");
280			painCave.severity = OPENMD_ERROR;
281			painCave.isFatal = 1;
282			simError();
283			}
284			if (!args_info.voxelSize_given) {
285			sprintf( painCave.errMsg,
286			"A voxel size must be specified when calculating"
287			" volume-resolved Tetrahedrality Parameters");
288			painCave.severity = OPENMD_ERROR;
289			painCave.isFatal = 1;
290			simError();
291			}
292			if (!args_info.gaussWidth_given) {
293			sprintf( painCave.errMsg,
294			"A gaussian width must be specified when calculating"
295			" volume-resolved Tetrahedrality Parameters");
296			painCave.severity = OPENMD_ERROR;
297			painCave.isFatal = 1;
298			simError();
299			}
300			analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
301			args_info.rcut_arg,
302			args_info.voxelSize_arg,
303			args_info.gaussWidth_arg);
304	gezelter	1992	} else if (args_info.ior_given){
305	gezelter	1513	if (args_info.rcut_given) {
306	gezelter	1992	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
307			args_info.rcut_arg,
308			args_info.nbins_arg, maxLen);
309			} else {
310			sprintf( painCave.errMsg,
311			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
312			painCave.severity = OPENMD_ERROR;
313			painCave.isFatal = 1;
314			simError();
315			}
316			} else if (args_info.for_given){
317			if (args_info.rcut_given) {
318			analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
319	kstocke1	1522	args_info.nbins_arg, maxLen);
320	chuckv	1445	} else {
321	gezelter	1513	sprintf( painCave.errMsg,
322	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
323	gezelter	1513	painCave.severity = OPENMD_ERROR;
324			painCave.isFatal = 1;
325			simError();
326			}
327			} else if (args_info.bad_given){
328			if (args_info.rcut_given) {
329	gezelter	1846	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
330			args_info.rcut_arg,
331	kstocke1	1522	args_info.nbins_arg);
332	gezelter	1513	} else {
333			sprintf( painCave.errMsg,
334	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
335	gezelter	1513	painCave.severity = OPENMD_ERROR;
336			painCave.isFatal = 1;
337			simError();
338	gezelter	1846	}
339	gezelter	1513	} else if (args_info.scd_given) {
340			if (batchMode) {
341	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
342			args_info.molname_arg,
343	kstocke1	1522	args_info.begin_arg, args_info.end_arg);
344	gezelter	1513	} else{
345			std::string sele3 = args_info.sele3_arg;
346	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
347			sele1, sele2, sele3);
348	gezelter	1513	}
349			}else if (args_info.density_given) {
350			analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
351	kstocke1	1522	args_info.nbins_arg);
352	gezelter	1513	} else if (args_info.count_given) {
353			analyser = new ObjectCount(info, dumpFileName, sele1 );
354			} else if (args_info.slab_density_given) {
355			analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
356	gezelter	1879	} else if (args_info.rnemdz_given) {
357			analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
358			} else if (args_info.rnemdr_given) {
359			analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
360	gezelter	1953	} else if (args_info.rnemdrt_given) {
361			analyser = new RNEMDRTheta(info, dumpFileName, sele1,
362			args_info.nbins_arg, args_info.nanglebins_arg);
363	gezelter	1994	} else if (args_info.nitrile_given) {
364			analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
365			args_info.nbins_arg);
366	gezelter	1513	} else if (args_info.p_angle_given) {
367	gezelter	1979	if (args_info.sele1_given) {
368			if (args_info.sele2_given)
369			analyser = new pAngle(info, dumpFileName, sele1, sele2,
370			args_info.nbins_arg);
371			else
372	gezelter	1991	if (args_info.seleoffset_given) {
373			if (args_info.seleoffset2_given) {
374			analyser = new pAngle(info, dumpFileName, sele1,
375			args_info.seleoffset_arg,
376			args_info.seleoffset2_arg,
377			args_info.nbins_arg);
378			} else {
379			analyser = new pAngle(info, dumpFileName, sele1,
380			args_info.seleoffset_arg,
381			args_info.nbins_arg);
382			}
383			} else
384	gezelter	1979	analyser = new pAngle(info, dumpFileName, sele1,
385			args_info.nbins_arg);
386			} else {
387			sprintf( painCave.errMsg,
388			"At least one selection script (--sele1) must be specified when "
389			"calculating P(angle) distributions");
390			painCave.severity = OPENMD_ERROR;
391			painCave.isFatal = 1;
392			simError();
393			}
394	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
395	gezelter	1513	}else if (args_info.hxy_given) {
396			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
397	kstocke1	1522	args_info.nbins_y_arg, args_info.nbins_arg);
398	gezelter	956	#endif
399	gezelter	1513	}else if (args_info.rho_r_given) {
400			if (args_info.radius_given){
401			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
402			}else{
403			sprintf( painCave.errMsg,
404	kstocke1	1522	"A particle radius (radius) must be specified when calculating Rho(r)");
405	gezelter	1513	painCave.severity = OPENMD_ERROR;
406			painCave.isFatal = 1;
407			simError();
408	chuckv	1091	}
409	kstocke1	1522	} else if (args_info.hullvol_given) {
410	gezelter	1513	analyser = new NanoVolume(info, dumpFileName, sele1);
411	gezelter	1585	} else if (args_info.rodlength_given) {
412			analyser = new NanoLength(info, dumpFileName, sele1);
413	kstocke1	1522	} else if (args_info.angle_r_given) {
414			analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
415	gezelter	1513	}
416	gezelter	1846
417	gezelter	1513	if (args_info.output_given) {
418			analyser->setOutputName(args_info.output_arg);
419			}
420			if (args_info.step_given) {
421			analyser->setStep(args_info.step_arg);
422			}
423	gezelter	1846
424	gezelter	1513	analyser->process();
425	kstocke1	1522
426	gezelter	1513	delete analyser;
427			delete info;
428	gezelter	1846
429	gezelter	1513	return 0;
430	tim	310	}