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"
#include "applications/staticProps/HBondGeometric.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);
  } else if (args_info.hbond_given){
    if (args_info.rcut_given) {
      if (args_info.thetacut_given) {
        
        analyser = new HBondGeometric(info, dumpFileName, sele1, sele2,
                                      args_info.rcut_arg,
                                      args_info.thetacut_arg,
                                      args_info.nbins_arg);
      } else {
        sprintf( painCave.errMsg,
                 "A cutoff angle (thetacut) must be specified when calculating Hydrogen Bonding Statistics");
        painCave.severity = OPENMD_ERROR;
        painCave.isFatal = 1;
        simError();
      }
    } else {
      sprintf( painCave.errMsg,
               "A cutoff radius (rcut) must be specified when calculating Hydrogen Bonding Statistics");
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal = 1;
      simError();
    }    
  }
  
  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:	2049
Committed:	Tue Jan 6 21:44:10 2015 UTC (10 years, 3 months ago) by gezelter
File size:	18843 byte(s)
Log Message:	Added Geometric HBond StaticProps module.
#	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	2049	#include "applications/staticProps/HBondGeometric.hpp"
86	gezelter	1879
87	gezelter	1390	using namespace OpenMD;
88	tim	310
89			int main(int argc, char* argv[]){
90
91	gezelter	1513
92			gengetopt_args_info args_info;
93
94			//parse the command line option
95			if (cmdline_parser (argc, argv, &args_info) != 0) {
96			exit(1) ;
97			}
98
99			//get the dumpfile name
100			std::string dumpFileName = args_info.input_arg;
101			std::string sele1;
102			std::string sele2;
103	gezelter	2023	std::string sele3;
104	gezelter	1513
105			// check the first selection argument, or set it to the environment
106			// variable, or failing that, set it to "select all"
107
108			if (args_info.sele1_given) {
109			sele1 = args_info.sele1_arg;
110			} else {
111			char* sele1Env= getenv("SELECTION1");
112			if (sele1Env) {
113			sele1 = sele1Env;
114			} else {
115			sele1 = "select all";
116			}
117			}
118
119			// check the second selection argument, or set it to the environment
120	gezelter	1937	// variable, or failing that, set it to the first selection
121	gezelter	1513
122			if (args_info.sele2_given) {
123			sele2 = args_info.sele2_arg;
124			} else {
125	gezelter	1937	char* sele2Env = getenv("SELECTION2");
126	gezelter	1513	if (sele2Env) {
127			sele2 = sele2Env;
128			} else {
129	gezelter	1819	//If sele2 is not specified, then the default behavior
130			//should be what is already intended for sele1
131	jmichalk	1785	sele2 = sele1;
132	gezelter	1513	}
133			}
134	gezelter	1846
135	gezelter	2023	// check the third selection argument, which is only set if
136			// requested by the user
137
138			if (args_info.sele3_given) sele3 = args_info.sele3_arg;
139
140	gezelter	1513	bool batchMode;
141			if (args_info.scd_given){
142	gezelter	1846	if (args_info.sele1_given &&
143			args_info.sele2_given && args_info.sele3_given) {
144	gezelter	1513	batchMode = false;
145	gezelter	1846	} else if (args_info.molname_given &&
146			args_info.begin_given && args_info.end_given) {
147			if (args_info.begin_arg < 0 \|\|
148			args_info.end_arg < 0 \|\| args_info.begin_arg > args_info.end_arg-2) {
149	gezelter	1513	sprintf( painCave.errMsg,
150			"below conditions are not satisfied:\n"
151			"0 <= begin && 0<= end && begin <= end-2\n");
152			painCave.severity = OPENMD_ERROR;
153			painCave.isFatal = 1;
154			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 = OPENMD_ERROR;
162			painCave.isFatal = 1;
163	gezelter	1846	simError();
164	gezelter	1513	}
165			}
166
167			//parse md file and set up the system
168			SimCreator creator;
169			SimInfo* info = creator.createSim(dumpFileName);
170	tim	310
171	gezelter	1513	RealType maxLen;
172			RealType zmaxLen;
173			if (args_info.length_given) {
174			maxLen = args_info.length_arg;
175			if (args_info.zlength_given){
176			zmaxLen = args_info.zlength_arg;
177	chuckv	1445	}
178	gezelter	1513	} else {
179			Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat();
180			maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0;
181			zmaxLen = hmat(2,2);
182			}
183	kstocke1	1522
184	gezelter	1513	StaticAnalyser* analyser;
185			if (args_info.gofr_given){
186			analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen,
187	kstocke1	1522	args_info.nbins_arg);
188	gezelter	1513	} else if (args_info.gofz_given) {
189			analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen,
190	kstocke1	1522	args_info.nbins_arg);
191	gezelter	1513	} else if (args_info.r_z_given) {
192			analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen,
193	kstocke1	1522	args_info.nbins_arg, args_info.nbins_z_arg);
194	gezelter	1513	} else if (args_info.r_theta_given) {
195	gezelter	2023	if (args_info.sele3_given)
196			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, sele3, maxLen,
197			args_info.nbins_arg, args_info.nanglebins_arg);
198			else
199			analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen,
200			args_info.nbins_arg, args_info.nanglebins_arg);
201	gezelter	1513	} else if (args_info.r_omega_given) {
202	gezelter	2023	if (args_info.sele3_given)
203			analyser = new GofROmega(info, dumpFileName, sele1, sele2, sele3, maxLen,
204			args_info.nbins_arg, args_info.nanglebins_arg);
205			else
206			analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen,
207			args_info.nbins_arg, args_info.nanglebins_arg);
208
209	gezelter	1513	} else if (args_info.theta_omega_given) {
210	gezelter	2023	if (args_info.sele3_given)
211			analyser = new GofAngle2(info, dumpFileName, sele1, sele2, sele3,
212			args_info.nanglebins_arg);
213			else
214			analyser = new GofAngle2(info, dumpFileName, sele1, sele2,
215			args_info.nanglebins_arg);
216	gezelter	1513	} else if (args_info.gxyz_given) {
217			if (args_info.refsele_given) {
218	gezelter	1846	analyser= new GofXyz(info, dumpFileName, sele1, sele2,
219			args_info.refsele_arg, maxLen, args_info.nbins_arg);
220	gezelter	1039	} else {
221	gezelter	1513	sprintf( painCave.errMsg,
222	kstocke1	1522	"--refsele must set when --gxyz is used");
223	gezelter	1513	painCave.severity = OPENMD_ERROR;
224			painCave.isFatal = 1;
225			simError();
226	tim	310	}
227	gezelter	1513	} else if (args_info.twodgofr_given){
228			if (args_info.dz_given) {
229			analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen,
230	kstocke1	1522	args_info.dz_arg, args_info.nbins_arg);
231	chuckv	1445	} else {
232	gezelter	1513	sprintf( painCave.errMsg,
233	kstocke1	1522	"A slab width (dz) must be specified when calculating TwoDGofR");
234	gezelter	1513	painCave.severity = OPENMD_ERROR;
235			painCave.isFatal = 1;
236			simError();
237	kstocke1	1522	}
238	gezelter	1513	} else if (args_info.p2_given) {
239	gezelter	1542	if (args_info.sele1_given) {
240			if (args_info.sele2_given)
241			analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2);
242			else
243	gezelter	1819	if (args_info.seleoffset_given)
244			analyser = new P2OrderParameter(info, dumpFileName, sele1,
245			args_info.seleoffset_arg);
246			else
247			analyser = new P2OrderParameter(info, dumpFileName, sele1);
248	gezelter	1542	} else {
249			sprintf( painCave.errMsg,
250			"At least one selection script (--sele1) must be specified when calculating P2 order parameters");
251			painCave.severity = OPENMD_ERROR;
252			painCave.isFatal = 1;
253			simError();
254			}
255	gezelter	1513	} else if (args_info.rp2_given){
256			analyser = new RippleOP(info, dumpFileName, sele1, sele2);
257			} else if (args_info.bo_given){
258			if (args_info.rcut_given) {
259			analyser = new BondOrderParameter(info, dumpFileName, sele1,
260	kstocke1	1522	args_info.rcut_arg,
261			args_info.nbins_arg);
262	gezelter	1513	} else {
263			sprintf( painCave.errMsg,
264	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
265	gezelter	1513	painCave.severity = OPENMD_ERROR;
266			painCave.isFatal = 1;
267			simError();
268	tim	544	}
269	gezelter	1998	} else if (args_info.multipole_given){
270	gezelter	1999	analyser = new MultipoleSum(info, dumpFileName, sele1,
271			maxLen, args_info.nbins_arg);
272	kstocke1	1522	} else if (args_info.tet_param_given) {
273			if (args_info.rcut_given) {
274			analyser = new TetrahedralityParam(info, dumpFileName, sele1,
275			args_info.rcut_arg,
276			args_info.nbins_arg);
277			} else {
278			sprintf( painCave.errMsg,
279			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
280			painCave.severity = OPENMD_ERROR;
281			painCave.isFatal = 1;
282			simError();
283			}
284	gezelter	1782	} else if (args_info.tet_param_z_given) {
285			if (args_info.rcut_given) {
286	gezelter	1846	analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2,
287			args_info.rcut_arg,
288			args_info.nbins_arg);
289	gezelter	1782	} else {
290			sprintf( painCave.errMsg,
291			"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters");
292			painCave.severity = OPENMD_ERROR;
293			painCave.isFatal = 1;
294			simError();
295			}
296	gezelter	2015	} else if (args_info.tet_param_xyz_given) {
297			if (!args_info.rcut_given) {
298			sprintf( painCave.errMsg,
299			"A cutoff radius (rcut) must be specified when calculating"
300			" Tetrahedrality Parameters");
301			painCave.severity = OPENMD_ERROR;
302			painCave.isFatal = 1;
303			simError();
304			}
305			if (!args_info.voxelSize_given) {
306			sprintf( painCave.errMsg,
307			"A voxel size must be specified when calculating"
308			" volume-resolved Tetrahedrality Parameters");
309			painCave.severity = OPENMD_ERROR;
310			painCave.isFatal = 1;
311			simError();
312			}
313			if (!args_info.gaussWidth_given) {
314			sprintf( painCave.errMsg,
315			"A gaussian width must be specified when calculating"
316			" volume-resolved Tetrahedrality Parameters");
317			painCave.severity = OPENMD_ERROR;
318			painCave.isFatal = 1;
319			simError();
320			}
321			analyser = new TetrahedralityParamXYZ(info, dumpFileName, sele1, sele2,
322			args_info.rcut_arg,
323			args_info.voxelSize_arg,
324			args_info.gaussWidth_arg);
325	gezelter	1992	} else if (args_info.ior_given){
326	gezelter	1513	if (args_info.rcut_given) {
327	gezelter	1992	analyser = new IcosahedralOfR(info, dumpFileName, sele1,
328			args_info.rcut_arg,
329			args_info.nbins_arg, maxLen);
330			} else {
331			sprintf( painCave.errMsg,
332			"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
333			painCave.severity = OPENMD_ERROR;
334			painCave.isFatal = 1;
335			simError();
336			}
337			} else if (args_info.for_given){
338			if (args_info.rcut_given) {
339			analyser = new FCCOfR(info, dumpFileName, sele1, args_info.rcut_arg,
340	kstocke1	1522	args_info.nbins_arg, maxLen);
341	chuckv	1445	} else {
342	gezelter	1513	sprintf( painCave.errMsg,
343	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters");
344	gezelter	1513	painCave.severity = OPENMD_ERROR;
345			painCave.isFatal = 1;
346			simError();
347			}
348			} else if (args_info.bad_given){
349			if (args_info.rcut_given) {
350	gezelter	1846	analyser = new BondAngleDistribution(info, dumpFileName, sele1,
351			args_info.rcut_arg,
352	kstocke1	1522	args_info.nbins_arg);
353	gezelter	1513	} else {
354			sprintf( painCave.errMsg,
355	kstocke1	1522	"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions");
356	gezelter	1513	painCave.severity = OPENMD_ERROR;
357			painCave.isFatal = 1;
358			simError();
359	gezelter	1846	}
360	gezelter	1513	} else if (args_info.scd_given) {
361			if (batchMode) {
362	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
363			args_info.molname_arg,
364	kstocke1	1522	args_info.begin_arg, args_info.end_arg);
365	gezelter	1513	} else{
366	gezelter	1846	analyser = new SCDOrderParameter(info, dumpFileName,
367			sele1, sele2, sele3);
368	gezelter	1513	}
369			}else if (args_info.density_given) {
370			analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen,
371	kstocke1	1522	args_info.nbins_arg);
372	gezelter	1513	} else if (args_info.count_given) {
373			analyser = new ObjectCount(info, dumpFileName, sele1 );
374			} else if (args_info.slab_density_given) {
375			analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg);
376	gezelter	1879	} else if (args_info.rnemdz_given) {
377			analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg);
378			} else if (args_info.rnemdr_given) {
379			analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg);
380	gezelter	1953	} else if (args_info.rnemdrt_given) {
381			analyser = new RNEMDRTheta(info, dumpFileName, sele1,
382			args_info.nbins_arg, args_info.nanglebins_arg);
383	gezelter	1994	} else if (args_info.nitrile_given) {
384			analyser = new NitrileFrequencyMap(info, dumpFileName, sele1,
385			args_info.nbins_arg);
386	gezelter	1513	} else if (args_info.p_angle_given) {
387	gezelter	1979	if (args_info.sele1_given) {
388			if (args_info.sele2_given)
389			analyser = new pAngle(info, dumpFileName, sele1, sele2,
390			args_info.nbins_arg);
391			else
392	gezelter	1991	if (args_info.seleoffset_given) {
393			if (args_info.seleoffset2_given) {
394			analyser = new pAngle(info, dumpFileName, sele1,
395			args_info.seleoffset_arg,
396			args_info.seleoffset2_arg,
397			args_info.nbins_arg);
398			} else {
399			analyser = new pAngle(info, dumpFileName, sele1,
400			args_info.seleoffset_arg,
401			args_info.nbins_arg);
402			}
403			} else
404	gezelter	1979	analyser = new pAngle(info, dumpFileName, sele1,
405			args_info.nbins_arg);
406			} else {
407			sprintf( painCave.errMsg,
408			"At least one selection script (--sele1) must be specified when "
409			"calculating P(angle) distributions");
410			painCave.severity = OPENMD_ERROR;
411			painCave.isFatal = 1;
412			simError();
413			}
414	gezelter	957	#if defined(HAVE_FFTW_H) \|\| defined(HAVE_DFFTW_H) \|\| defined(HAVE_FFTW3_H)
415	gezelter	1513	}else if (args_info.hxy_given) {
416			analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg,
417	kstocke1	1522	args_info.nbins_y_arg, args_info.nbins_arg);
418	gezelter	956	#endif
419	jmichalk	2031	}else if (args_info.surfDiffusion_given){
420			analyser = new SurfaceDiffusion(info, dumpFileName, sele1, maxLen);
421	gezelter	1513	}else if (args_info.rho_r_given) {
422			if (args_info.radius_given){
423			analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg);
424			}else{
425			sprintf( painCave.errMsg,
426	kstocke1	1522	"A particle radius (radius) must be specified when calculating Rho(r)");
427	gezelter	1513	painCave.severity = OPENMD_ERROR;
428			painCave.isFatal = 1;
429			simError();
430	chuckv	1091	}
431	kstocke1	1522	} else if (args_info.hullvol_given) {
432	gezelter	1513	analyser = new NanoVolume(info, dumpFileName, sele1);
433	gezelter	1585	} else if (args_info.rodlength_given) {
434			analyser = new NanoLength(info, dumpFileName, sele1);
435	kstocke1	1522	} else if (args_info.angle_r_given) {
436			analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg);
437	gezelter	2049	} else if (args_info.hbond_given){
438			if (args_info.rcut_given) {
439			if (args_info.thetacut_given) {
440
441			analyser = new HBondGeometric(info, dumpFileName, sele1, sele2,
442			args_info.rcut_arg,
443			args_info.thetacut_arg,
444			args_info.nbins_arg);
445			} else {
446			sprintf( painCave.errMsg,
447			"A cutoff angle (thetacut) must be specified when calculating Hydrogen Bonding Statistics");
448			painCave.severity = OPENMD_ERROR;
449			painCave.isFatal = 1;
450			simError();
451			}
452			} else {
453			sprintf( painCave.errMsg,
454			"A cutoff radius (rcut) must be specified when calculating Hydrogen Bonding Statistics");
455			painCave.severity = OPENMD_ERROR;
456			painCave.isFatal = 1;
457			simError();
458			}
459	gezelter	1513	}
460	gezelter	1846
461	gezelter	1513	if (args_info.output_given) {
462			analyser->setOutputName(args_info.output_arg);
463			}
464			if (args_info.step_given) {
465			analyser->setStep(args_info.step_arg);
466			}
467	gezelter	1846
468	gezelter	1513	analyser->process();
469	kstocke1	1522
470	gezelter	1513	delete analyser;
471			delete info;
472	gezelter	1846
473	gezelter	1513	return 0;
474	tim	310	}