List of output files for PATHSAMPLE: Difference between revisions

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'''Input Structures'''
'''Input Structures'''


start.<n> input coordinate files for OPTIM generated via pathsample
start.<n> -- input coordinate files for OPTIM generated via pathsample


finish.<n> input coordinate files for OPTIM generated via pathsample
finish.<n> -- input coordinate files for OPTIM generated via pathsample


'''Input'''
'''Input'''


pathdath - file for pathsample
pathdath -- file for pathsample


pathdata.change - file read in during pathsample run to change parameters whilst the job is running
pathdata.change -- file read in during pathsample run to change parameters whilst the job is running


odata.start - OPTIM data file for initial frequency calc for start file
odata.start -- OPTIM data file for initial frequency calc for start file
odata.finish - OPTIM data file for initial frequency calc for finish file
odata.finish -- OPTIM data file for initial frequency calc for finish file


odata.connect - OPTIM data file for CONNECT run
odata.connect -- OPTIM data file for CONNECT run


odata.new.<n> - files generated by OPTIM for restarting from that point
odata.new.<n> -- files generated by OPTIM for restarting from that point


odata.<n> - OPTIM input file created by pathsample
odata.<n> -- OPTIM input file created by pathsample


min.data.info.<n> - coordinate input files for input minima created by OPTIM for PATHSAMPLE
min.data.info.<n> -- coordinate input files for input minima created by OPTIM for PATHSAMPLE


path.info.data.<n> - min.ts.min triple with frequencies, and structures created by OPTIM for PATHSAMPLE
path.info.data.<n> -- min.ts.min triple with frequencies, and structures created by OPTIM for PATHSAMPLE


nodes.info - processor addresses for a distributed memory machine
nodes.info -- processor addresses for a distributed memory machine


'''Output'''
'''Output'''


OPTIM.connect.<n> - output from OPTIM runs
OPTIM.connect.<n> -- output from OPTIM runs


min.A, min.B and min.data -- A, B and intermediate minima, respectively
min.A, min.B and min.data -- A, B and intermediate minima, respectively
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ts.data -- transition states
ts.data -- transition states


<file>.fastest -- GT data for the fastest connection of the database
<file>.fastest -- GT data for the fastest connection of the database


<file>.regrouped -- data after regrouping into free energy groups
<file>.regrouped -- data after regrouping into free energy groups


<file>.retained -- stationary point data retained after pruning via RETAINSP keyword
<file>.retained -- stationary point data retained after pruning via RETAINSP keyword


<file>.removed -- stationary point data retained after pruning via REMOVESP keyword
<file>.removed -- stationary point data retained after pruning via REMOVESP keyword


points.min, points.ts -- unformatted direct access file versions of min.data and ts.data
points.min, points.ts -- unformatted direct access file versions of min.data and ts.data


path.<n>.xyz -- path coordinates for path <n> in Xmakemol format produced with debugging on
path.<n>.xyz -- path coordinates for path <n> in Xmakemol format produced with debugging on

Revision as of 21:24, 1 August 2008

Input Structures

start.<n> -- input coordinate files for OPTIM generated via pathsample

finish.<n> -- input coordinate files for OPTIM generated via pathsample

Input

pathdath -- file for pathsample

pathdata.change -- file read in during pathsample run to change parameters whilst the job is running

odata.start -- OPTIM data file for initial frequency calc for start file

odata.finish -- OPTIM data file for initial frequency calc for finish file

odata.connect -- OPTIM data file for CONNECT run

odata.new.<n> -- files generated by OPTIM for restarting from that point

odata.<n> -- OPTIM input file created by pathsample

min.data.info.<n> -- coordinate input files for input minima created by OPTIM for PATHSAMPLE

path.info.data.<n> -- min.ts.min triple with frequencies, and structures created by OPTIM for PATHSAMPLE

nodes.info -- processor addresses for a distributed memory machine

Output

OPTIM.connect.<n> -- output from OPTIM runs

min.A, min.B and min.data -- A, B and intermediate minima, respectively

ts.data -- transition states

<file>.fastest -- GT data for the fastest connection of the database

<file>.regrouped -- data after regrouping into free energy groups

<file>.retained -- stationary point data retained after pruning via RETAINSP keyword

<file>.removed -- stationary point data retained after pruning via REMOVESP keyword

points.min, points.ts -- unformatted direct access file versions of min.data and ts.data

path.<n>.xyz -- path coordinates for path <n> in Xmakemol format produced with debugging on

path.xyz -- total path coordinates in Xmakemol format produced with debugging on

energies -- ?????

Misc

ts.attempts -- records TS where short cut paths have already been completed

commit.data -- committor probabilities for the minima

pairs.data -- record of connection attempts already performed

min.done -- record of minima from UNTRAP runs

redopoints -- ?????

extractedmin.crd -- ????

Epath -- ????

--mp466 10:31, 8 July 2008 (BST)