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"
#include "applications/staticProps/SurfaceDiffusion.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;
  std::string sele3;
  
  // 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;
    }
  }

  // check the third selection argument, which is only set if
  // requested by the user

  if (args_info.sele3_given) sele3 = args_info.sele3_arg;

  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) {
    if (args_info.sele3_given) 
      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
                                args_info.nbins_arg, args_info.nanglebins_arg);
    else 
      analyser  = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, 
                                args_info.nbins_arg, args_info.nanglebins_arg);
  } else if (args_info.r_omega_given) {
    if (args_info.sele3_given) 
      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
                                args_info.nbins_arg, args_info.nanglebins_arg);
    else 
      analyser  = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
                                args_info.nbins_arg, args_info.nanglebins_arg);

  } else if (args_info.theta_omega_given) {
    if (args_info.sele3_given) 
      analyser  = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
                                args_info.nanglebins_arg);
    else
      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{
      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.surfDiffusion_given){
    analyser = new SurfaceDiffusion(info, dumpFileName, sele1, maxLen);
  }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:	2031
Committed:	Fri Oct 31 18:40:40 2014 UTC (10 years, 6 months ago) by jmichalk
File size:	17915 byte(s)
Log Message:	Added a surface diffusion analyser to staticProps
#	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	jmichalk	2031	#include "applications/staticProps/SurfaceDiffusion.hpp"
85	gezelter	1879
86	gezelter	1390	using namespace OpenMD;
87	tim	310
88			int main(int argc, char* argv[]){
89
90	gezelter	1513
91			gengetopt_args_info args_info;
92
93			//parse the command line option
94			if (cmdline_parser (argc, argv, &args_info) != 0) {
95			exit(1) ;
96			}
97
98			//get the dumpfile name
99			std::string dumpFileName = args_info.input_arg;
100			std::string sele1;
101			std::string sele2;
102	gezelter	2023	std::string sele3;
103	gezelter	1513
104			// check the first selection argument, or set it to the environment
105			// variable, or failing that, set it to "select all"
106
107			if (args_info.sele1_given) {
108			sele1 = args_info.sele1_arg;
109			} else {
110			char* sele1Env= getenv("SELECTION1");
111			if (sele1Env) {
112			sele1 = sele1Env;
113			} else {
114			sele1 = "select all";
115			}
116			}
117
118			// check the second selection argument, or set it to the environment
119	gezelter	1937	// variable, or failing that, set it to the first selection
120	gezelter	1513
121			if (args_info.sele2_given) {
122			sele2 = args_info.sele2_arg;
123			} else {
124	gezelter	1937	char* sele2Env = getenv("SELECTION2");
125	gezelter	1513	if (sele2Env) {
126			sele2 = sele2Env;
127			} else {
128	gezelter	1819	//If sele2 is not specified, then the default behavior
129			//should be what is already intended for sele1
130	jmichalk	1785	sele2 = sele1;
131	gezelter	1513	}
132			}
133	gezelter	1846
134	gezelter	2023	// check the third selection argument, which is only set if
135			// requested by the user
136
137			if (args_info.sele3_given) sele3 = args_info.sele3_arg;
138
139	gezelter	1513	bool batchMode;
140			if (args_info.scd_given){
141	gezelter	1846	if (args_info.sele1_given &&
142			args_info.sele2_given && args_info.sele3_given) {
143	gezelter	1513	batchMode = false;
144	gezelter	1846	} else if (args_info.molname_given &&
145			args_info.begin_given && args_info.end_given) {
146			if (args_info.begin_arg < 0 \|\|
147			args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
148	gezelter	1513	sprintf( painCave.errMsg,
149			"below conditions are not satisfied:\n"
150			"0 <= begin && 0<= end && begin <= end-2\n");
151			painCave.severity = OPENMD_ERROR;
152			painCave.isFatal = 1;
153			simError();
154			}
155			batchMode = true;
156			} else{
157			sprintf( painCave.errMsg,
158			"either --sele1, --sele2, --sele3 are specified,"
159			" or --molname, --begin, --end are specified\n");
160			painCave.severity = OPENMD_ERROR;
161			painCave.isFatal = 1;
162	gezelter	1846	simError();
163	gezelter	1513	}
164			}
165
166			//parse md file and set up the system
167			SimCreator creator;
168			SimInfo* info = creator.createSim(dumpFileName);
169	tim	310
170	gezelter	1513	RealType maxLen;
171			RealType zmaxLen;
172			if (args_info.length_given) {
173			maxLen = args_info.length_arg;
174			if (args_info.zlength_given){
175			zmaxLen = args_info.zlength_arg;
176	chuckv	1445	}
177	gezelter	1513	} else {
178			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
179			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
180			zmaxLen = hmat(2,2);
181			}
182	kstocke1	1522
183	gezelter	1513	StaticAnalyser* analyser;
184			if (args_info.gofr_given){
185			analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
186	kstocke1	1522	args_info.nbins_arg);
187	gezelter	1513	} else if (args_info.gofz_given) {
188			analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
189	kstocke1	1522	args_info.nbins_arg);
190	gezelter	1513	} else if (args_info.r_z_given) {
191			analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
192	kstocke1	1522	args_info.nbins_arg, args_info.nbins_z_arg);
193	gezelter	1513	} else if (args_info.r_theta_given) {
194	gezelter	2023	if (args_info.sele3_given)
195			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
196			args_info.nbins_arg, args_info.nanglebins_arg);
197			else
198			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
199			args_info.nbins_arg, args_info.nanglebins_arg);
200	gezelter	1513	} else if (args_info.r_omega_given) {
201	gezelter	2023	if (args_info.sele3_given)
202			analyser = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
203			args_info.nbins_arg, args_info.nanglebins_arg);
204			else
205			analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
206			args_info.nbins_arg, args_info.nanglebins_arg);
207
208	gezelter	1513	} else if (args_info.theta_omega_given) {
209	gezelter	2023	if (args_info.sele3_given)
210			analyser = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
211			args_info.nanglebins_arg);
212			else
213			analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
214			args_info.nanglebins_arg);
215	gezelter	1513	} else if (args_info.gxyz_given) {
216			if (args_info.refsele_given) {
217	gezelter	1846	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
218			args_info.refsele_arg, maxLen, args_info.nbins_arg);
219	gezelter	1039	} else {
220	gezelter	1513	sprintf( painCave.errMsg,
221	kstocke1	1522	"--refsele must set when --gxyz is used");
222	gezelter	1513	painCave.severity = OPENMD_ERROR;
223			painCave.isFatal = 1;
224			simError();
225	tim	310	}
226	gezelter	1513	} else if (args_info.twodgofr_given){
227			if (args_info.dz_given) {
228			analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
229	kstocke1	1522	args_info.dz_arg, args_info.nbins_arg);
230	chuckv	1445	} else {
231	gezelter	1513	sprintf( painCave.errMsg,
232	kstocke1	1522	"A slab width (dz) must be specified when calculating TwoDGofR");
233	gezelter	1513	painCave.severity = OPENMD_ERROR;
234			painCave.isFatal = 1;
235			simError();
236	kstocke1	1522	}
237	gezelter	1513	} else if (args_info.p2_given) {
238	gezelter	1542	if (args_info.sele1_given) {
239			if (args_info.sele2_given)
240			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
241			else
242	gezelter	1819	if (args_info.seleoffset_given)
243			analyser = new P2OrderParameter(info, dumpFileName, sele1,
244			args_info.seleoffset_arg);
245			else
246			analyser = new P2OrderParameter(info, dumpFileName, sele1);
247	gezelter	1542	} else {
248			sprintf( painCave.errMsg,
249			"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
250			painCave.severity = OPENMD_ERROR;
251			painCave.isFatal = 1;
252			simError();
253			}
254	gezelter	1513	} else if (args_info.rp2_given){
255			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
256			} else if (args_info.bo_given){
257			if (args_info.rcut_given) {
258			analyser = new BondOrderParameter(info, dumpFileName, sele1,
259	kstocke1	1522	args_info.rcut_arg,
260			args_info.nbins_arg);
261	gezelter	1513	} else {
262			sprintf( painCave.errMsg,
263	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
264	gezelter	1513	painCave.severity = OPENMD_ERROR;
265			painCave.isFatal = 1;
266			simError();
267	tim	544	}
268	gezelter	1998	} else if (args_info.multipole_given){
269	gezelter	1999	analyser = new MultipoleSum(info, dumpFileName, sele1,
270			maxLen, args_info.nbins_arg);
271	kstocke1	1522	} else if (args_info.tet_param_given) {
272			if (args_info.rcut_given) {
273			analyser = new TetrahedralityParam(info, dumpFileName, sele1,
274			args_info.rcut_arg,
275			args_info.nbins_arg);
276			} else {
277			sprintf( painCave.errMsg,
278			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
279			painCave.severity = OPENMD_ERROR;
280			painCave.isFatal = 1;
281			simError();
282			}
283	gezelter	1782	} else if (args_info.tet_param_z_given) {
284			if (args_info.rcut_given) {
285	gezelter	1846	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
286			args_info.rcut_arg,
287			args_info.nbins_arg);
288	gezelter	1782	} else {
289			sprintf( painCave.errMsg,
290			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
291			painCave.severity = OPENMD_ERROR;
292			painCave.isFatal = 1;
293			simError();
294			}
295	gezelter	2015	} else if (args_info.tet_param_xyz_given) {
296			if (!args_info.rcut_given) {
297			sprintf( painCave.errMsg,
298			"A cutoff radius (rcut) must be specified when calculating"
299			" Tetrahedrality Parameters");
300			painCave.severity = OPENMD_ERROR;
301			painCave.isFatal = 1;
302			simError();
303			}
304			if (!args_info.voxelSize_given) {
305			sprintf( painCave.errMsg,
306			"A voxel size must be specified when calculating"
307			" volume-resolved Tetrahedrality Parameters");
308			painCave.severity = OPENMD_ERROR;
309			painCave.isFatal = 1;
310			simError();
311			}
312			if (!args_info.gaussWidth_given) {
313			sprintf( painCave.errMsg,
314			"A gaussian width must be specified when calculating"
315			" volume-resolved Tetrahedrality Parameters");
316			painCave.severity = OPENMD_ERROR;
317			painCave.isFatal = 1;
318			simError();
319			}
320			analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
321			args_info.rcut_arg,
322			args_info.voxelSize_arg,
323			args_info.gaussWidth_arg);
324	gezelter	1992	} else if (args_info.ior_given){
325	gezelter	1513	if (args_info.rcut_given) {
326	gezelter	1992	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
327			args_info.rcut_arg,
328			args_info.nbins_arg, maxLen);
329			} else {
330			sprintf( painCave.errMsg,
331			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
332			painCave.severity = OPENMD_ERROR;
333			painCave.isFatal = 1;
334			simError();
335			}
336			} else if (args_info.for_given){
337			if (args_info.rcut_given) {
338			analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
339	kstocke1	1522	args_info.nbins_arg, maxLen);
340	chuckv	1445	} else {
341	gezelter	1513	sprintf( painCave.errMsg,
342	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
343	gezelter	1513	painCave.severity = OPENMD_ERROR;
344			painCave.isFatal = 1;
345			simError();
346			}
347			} else if (args_info.bad_given){
348			if (args_info.rcut_given) {
349	gezelter	1846	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
350			args_info.rcut_arg,
351	kstocke1	1522	args_info.nbins_arg);
352	gezelter	1513	} else {
353			sprintf( painCave.errMsg,
354	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
355	gezelter	1513	painCave.severity = OPENMD_ERROR;
356			painCave.isFatal = 1;
357			simError();
358	gezelter	1846	}
359	gezelter	1513	} else if (args_info.scd_given) {
360			if (batchMode) {
361	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
362			args_info.molname_arg,
363	kstocke1	1522	args_info.begin_arg, args_info.end_arg);
364	gezelter	1513	} else{
365	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
366			sele1, sele2, sele3);
367	gezelter	1513	}
368			}else if (args_info.density_given) {
369			analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
370	kstocke1	1522	args_info.nbins_arg);
371	gezelter	1513	} else if (args_info.count_given) {
372			analyser = new ObjectCount(info, dumpFileName, sele1 );
373			} else if (args_info.slab_density_given) {
374			analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
375	gezelter	1879	} else if (args_info.rnemdz_given) {
376			analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
377			} else if (args_info.rnemdr_given) {
378			analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
379	gezelter	1953	} else if (args_info.rnemdrt_given) {
380			analyser = new RNEMDRTheta(info, dumpFileName, sele1,
381			args_info.nbins_arg, args_info.nanglebins_arg);
382	gezelter	1994	} else if (args_info.nitrile_given) {
383			analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
384			args_info.nbins_arg);
385	gezelter	1513	} else if (args_info.p_angle_given) {
386	gezelter	1979	if (args_info.sele1_given) {
387			if (args_info.sele2_given)
388			analyser = new pAngle(info, dumpFileName, sele1, sele2,
389			args_info.nbins_arg);
390			else
391	gezelter	1991	if (args_info.seleoffset_given) {
392			if (args_info.seleoffset2_given) {
393			analyser = new pAngle(info, dumpFileName, sele1,
394			args_info.seleoffset_arg,
395			args_info.seleoffset2_arg,
396			args_info.nbins_arg);
397			} else {
398			analyser = new pAngle(info, dumpFileName, sele1,
399			args_info.seleoffset_arg,
400			args_info.nbins_arg);
401			}
402			} else
403	gezelter	1979	analyser = new pAngle(info, dumpFileName, sele1,
404			args_info.nbins_arg);
405			} else {
406			sprintf( painCave.errMsg,
407			"At least one selection script (--sele1) must be specified when "
408			"calculating P(angle) distributions");
409			painCave.severity = OPENMD_ERROR;
410			painCave.isFatal = 1;
411			simError();
412			}
413	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
414	gezelter	1513	}else if (args_info.hxy_given) {
415			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
416	kstocke1	1522	args_info.nbins_y_arg, args_info.nbins_arg);
417	gezelter	956	#endif
418	jmichalk	2031	}else if (args_info.surfDiffusion_given){
419			analyser = new SurfaceDiffusion(info, dumpFileName, sele1, maxLen);
420	gezelter	1513	}else if (args_info.rho_r_given) {
421			if (args_info.radius_given){
422			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
423			}else{
424			sprintf( painCave.errMsg,
425	kstocke1	1522	"A particle radius (radius) must be specified when calculating Rho(r)");
426	gezelter	1513	painCave.severity = OPENMD_ERROR;
427			painCave.isFatal = 1;
428			simError();
429	chuckv	1091	}
430	kstocke1	1522	} else if (args_info.hullvol_given) {
431	gezelter	1513	analyser = new NanoVolume(info, dumpFileName, sele1);
432	gezelter	1585	} else if (args_info.rodlength_given) {
433			analyser = new NanoLength(info, dumpFileName, sele1);
434	kstocke1	1522	} else if (args_info.angle_r_given) {
435			analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
436	gezelter	1513	}
437	gezelter	1846
438	gezelter	1513	if (args_info.output_given) {
439			analyser->setOutputName(args_info.output_arg);
440			}
441			if (args_info.step_given) {
442			analyser->setStep(args_info.step_arg);
443			}
444	gezelter	1846
445	gezelter	1513	analyser->process();
446	kstocke1	1522
447	gezelter	1513	delete analyser;
448			delete info;
449	gezelter	1846
450	gezelter	1513	return 0;
451	tim	310	}