analysis

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Purpose

The analysis command is used to indicate that a structure-based quantity should be calculated using either the molecular system read from the .car coordinate file or data obtained from history or archive files. Output is directed to a graph file in the standard .tbl format.

Syntax

analysis ?keyword = value? ...



Keyword   Values              Default	          Meaning


method    voronoi             voronoi       Voronoi tessellation statistics.
          pair_c*orrelation_function        g(r) calculation.  
          mean_s*quare_displacement         Atom mean-square displacement.
          cohesive_*energy
          elastic_d*ynamic
          elastic_s*tatic
          length_dist*ribution
          angle_dist*ribution
          dihedral_dist*ribution
          radius_of_gyr_dist*ribution
          nonbond_dist*ribution
          orientational_corr*elation
          velocity_acf
          dipole_acf
          local_mode*_analysis
          vdw_vol*ume_distribution
          free_vol*ume_distribution
          atomic_s*tresses

frame_def*inition
          string              --            Name of a file containing a 
                                            specification of a Discover .arc or 
                                            .his file and the frames to be used
                                            in the analysis.

subset    string              --            Name of the atom set to be used in 
                                            the analysis. The atom set must
                                            be present in the .mdf file.

subset2   string              --            Optional second atom set to be used 
                                            when a pair correlation function 
                                            is to be calculated.

table     Boolean             false         Write output to a table file.

file*name string              run_name.tbl  Name of the .tbl file to receive 
                                            the output.

Description

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The analysis command is used to perform analysis on the current molecular system or on structures that were previously saved in .arc or .his files. In general, it is used to perform analysis on a subset of the atoms in the system, although the absence of a subset name is taken to mean that all atoms should be used.

The quantities that can be calculated are the pair correlation function (radial distribution function), the mean-square displacement of atoms in a previously-generated dynamics run, and statistics for the Voronoi tessellation of the system. For Voronoi statistics, the simulated system must be periodic. For details on theory and application relevant to this command, please consult Chapter 3 of the Polymer User Guide, the Amorphous_Cell module. All output is written to standard .tbl files.

Several restrictions apply to the use of this command:

For periodic systems, the cell must be orthorhombic.
For calculating mean-square displacements, the dynamics trajectory must be stored in a .his file.

Example

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analysis method = pair_correlation_function \ 
 	 frame_definition = helium_neon.fdef subset = he \ 
 	 subset2 = ne +table filename = helium_neon_pcf.tbl

This example of the analysis command means to calculate all the component pair correlation functions in a simulated mixture of helium and neon, using configurations of the system that have been stored in a .his or .arc file. The actual filename and specification of the frames to be used is given in the file helium_neon.fdef; for example:

helium_neon.arc 
 3 
 1 
 2 
 3

indicates that configurations 1, 2, and 3 from the file helium_neon.arc are to be used.

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List of BTCL commands analyzeNonbond command