print

Jump to Description or Examples; explanation of how commands are documented.

Purpose

The print command is used to write out information for various system properties, for example, the energy, structure, and thermodynamic state.

The information chosen can be printed to an archive, output, table, or history file. When it appears as part of the minimize or dynamics command (in an execute structure), the requested information is printed as the minimization or dynamics run proceeds.

Currently, the print command must be part of a minimize or dynamics command--a print command issued directly from the BTCL prompt or in a source file does not do anything.

Syntax

print filetype ?path? ?keyword = value?...

Click to jump to the desired printing specifications:

Controlling where to print (file names and types)
Controlling type of printing (mainly control of averaging)
Controlling what properties to print

Path/Keyword Values Default Meaning

controlling where to print:

Jump to top of page

filetype out*put output Specify type of file to receive the arc*hive requested information. One of these table values must be the first argument after or tbl print, since the filetype is specified his*tory by a positional argument. Subsequent parameters have defaults that may depend on the filetype specified. file*name string run_name.extension User-defined name of archive, output, table, or history file. The default is the current run name with the appropriate extension--.arc for archive, .out for output, .tbl for table, or .his for history files, respectively.

controlling type of printing:

Jump to top of page

average Boolean false Print running average of the property. running_sd Boolean false Print running standard deviation of the property (available only for table file). batch_a*verage Boolean false Print batch average of the property. batch_s*ize integer 10 Size of the window used in batch averaging. batch_sd Boolean false Print batch standard deviation of the property (available only for table file). instant*aneous Boolean false Print instantaneous value of the property.

controlling what properties to print:

Jump to top of page

archive Pathname to parameters that may be printed only to archive files. coord*inates Boolean false Cartesian coordinates representing the structure (default is true if filetype = archive). deriv*ative Boolean false First derivatives of total potential energy with respect to Cartesian coordinates (only to archive file). vel*ocity Boolean false Velocities of the atoms (only to archive file and in dynamics only). energy*_summary Boolean false Equivalent to specifying total_energy, kinetic_energy, and potential_energy. total_e*nergy Boolean false Sum of kinetic and potential energy. kinetic_e*nergy Boolean false Kinetic energy, meaningful only in dynamics. potential_e*nergy Boolean false Potential energy. internal_e*nergy Boolean false Equivalent to specifying total_internal_energy, bond_energy, angle_energy, torsion_energy, oop_energy, and cross_term_energy. total_internal_e*nergy Boolean false Total internal energy, including both diagonal (bond, angle, torsion, oop) and non-diagonal (cross) terms. bond_e*nergy Boolean false Energy from all bond terms. angle_e*nergy Boolean false Energy from all bond angle terms. torsion_e*nergy Boolean false Energy from all dihedral angle terms. oop_e*nergy Boolean false Energy from all out-of-plane angle terms. cross_term_e*nergy Boolean false Energy from all cross terms. nonbond_e*nergy Boolean false Equivalent to specifying total_nonbond_energy, vdw_energy, dispersive_vdw_energy, repulsive_vdw_energy, coulomb_energy, and hbond_energy. total_nonbond_e*nergy Boolean false Energy of all interactions through space (within the cutoff distance, if any). vdw_e*nergy Boolean false Energy of all van der Waals interactions (within the cutoff distance, if any). disp*ersive_vdw_energy Boolean false Dispersive van der Waals energy. repul*sive_vdw_energy Boolean false Repulsive van der Waals energy. coulomb_e*nergy Boolean false Electrostatic energy (within the cutoff distance, if any). cell Boolean false Equivalent to specifying cell_a, cell_alpha, cell_b, cell_beta, cell_c, and cell_gamma. All these are meaningful only with periodic boundary conditions and only for dynamics. cell_a Boolean false Length of side a of unit cell. cell_b Boolean false Length of side b of unit cell. cell_c Boolean false Length of side c of unit cell. cell_alpha Boolean false Angle alpha (between b and c) of the cell. cell_beta Boolean false Angle beta (between a and c) of the cell. cell_gamma Boolean false Angle gamma (between a and b) of the cell. state Boolean false Equivalent to specifying temperature, pressure, volume, and density. Temperature is meaningful only in dynamics; pressure, volume, and density are meaningful only in periodic systems and only in dynamics. tempe*rature Boolean false Temperature. pressure Boolean false Pressure. volume Boolean false Volume. density Boolean false Density. stress Boolean false Equivalent to specifying sxx, syy, szz, syz, sxz, and sxy. Diagonal terms (sxx, syy, szz) of stress tensor are also called tensile stress; off-diagonal terms (syz, sxz, sxy) of stress tensor are also called shear stress. Meaningful only with periodic systems and only in dynamics. sxx Boolean false xx component of stress tensor. syy Boolean false yy component of stress tensor. szz Boolean false zz component of stress tensor. syz Boolean false yz component of stress tensor. sxz Boolean false xz component of stress tensor. sxy Boolean false xy component of stress tensor. strain Boolean false Equivalent to specifying exx, exy, exz, eyy, eyz, and ezz. Diagonal terms (exx, eyy, ezz) of strain tensor are also called tensile strain; off-diagonal terms (eyz, exz, exy) of strain tensor are also called shear strain. Meaningful only with periodic systems and only in dynamics. exx Boolean false xx component of strain tensor. eyy Boolean false yy component of strain tensor. ezz Boolean false zz component of strain tensor. eyz Boolean false yz component of strain tensor. exz Boolean false xz component of strain tensor. exy Boolean false xy component of strain tensor.

Description

Jump to Syntax or Examples

Minimization and dynamics usually print only a summary at the beginning and after completion, to the standard output file. The print command is used to obtain additional information and to place it in the archive, output or table files.

A single print command can print to only one of these three places. However, a dynamics or minimize command may have multiple print commands. If the filename keyword is specified, that filename is used; otherwise, output filenames are defaulted to:

archive: run_name.arc
output: run_name.out
table: run_name.tbl
history: run_name.his

where run_name is your name for the calculation. Coordinates, velocities and derivatives can be printed out only in archive files. Other properties given can be specified only for an output or table file. If velocities and derivatives are printed out, the print command should give file extensions of .vel and .der, to prevent the .arc file from being overwritten.

Only instantaneous values can be printed out for coordinates, velocities, and derivatives. For other properties, instantaneous values, running averages, and batch averages can be printed out during dynamics in both the standard output file and the table file. Standard deviations for both the running sum and the batch sum can be printed out only in the table file.

If you do not specify the type of averages to be printed in the standard output and table file, the default is to print both running and batch averages in the standard output and instantaneous values in the table file.

The running average includes every value computed thus far, not just values encountered at the specified frequency; i.e., the frequency (keyword for the execute statement) is the printout frequency, not the calculation's step frequency. For batch averages, batch size is the number of steps to be used. If the batch size is n, the window consists of the last n steps (or all steps if there are fewer than n).

When the filetype selected is history, only the filename parameter is noticed by the print command. History files are similar to binary archive files and contain a fixed set of information which can be read by the Insight II interface.

Example 1

Jump to Syntax or Description

minimize execute +before +after frequency = 10 \ 
 	 command = {print output +energy_summary}

This example of the print command means to run the minimizer with its default settings and to print the energy summary to the output file before minimization starts, every 10 steps during the minimization, and after the end of the run.

Example 2

dynamics time = 300 execute frequency = 10 \ 
 	 first_step = 20 last_step = 200 \ 
 	 command = {print table file = summary.tbl \ 
 	 +energy_summary +state +average +average_sd} \ 
 	 execute frequency = 20 command = \ 
 	 {print archive +coordinates}

This example of the print command means to run dynamics for 300 fs and to print the energy summary and the state information to the table file summary.tbl, starting at step 30 (20 + 10) and continuing every 10 steps until step 200; also, write the coordinates to the archive file run_name.arc every 20 steps.

Main access page

Advanced-Use access.

List of BTCL commands peek command pseudoAtom command