Df398 at 10:45, 17 November 2020

2020-11-17T10:45:09Z

← Older revision		Revision as of 10:45, 17 November 2020
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	'''odata.connect'''		'''odata.connect'''

	! DEBUG		! DEBUG<br />
	NEWCONNECT 1 1 2.0 25.0 10 1.0 0.001<br />		NEWCONNECT 1 1 2.0 25.0 10 1.0 0.001<br />
	NEWNEB 30 500 0.0001<br />		NEWNEB 30 500 0.0001<br />
Line 236:		Line 236:
	'''Step 5.''' pathdata file should contain the DIJINITSTART keyword to start an initial connection job and produce the database files (min.data, ts.data, points.min and points.ts).<br />		'''Step 5.''' pathdata file should contain the DIJINITSTART keyword to start an initial connection job and produce the database files (min.data, ts.data, points.min and points.ts).<br />

	For example, an ~~odata.connect~~ file (that uses the DFTBP potential) could be of the form:		For example, a pathdata file (that uses the DFTBP potential) could be of the form:

	'''~~odata.connect~~:'''		'''pathdata:'''

	EXEC ~/svn/OPTIM/builds/ifort_64_2019_5_281/DFTBPOPTIM<br />		EXEC ~/svn/OPTIM/builds/ifort_64_2019_5_281/DFTBPOPTIM<br />

Df398: This page describes how to perform initial connection jobs with PATHSAMPLE (assuming no path.info or min.data.info files are present)

2020-07-10T23:43:23Z

This page describes how to perform initial connection jobs with PATHSAMPLE (assuming no path.info or min.data.info files are present)

New page

This file describes how to perform initial connection jobs with PATHSAMPLE. There are several options depending on the potential that is being used. These instructions assume that you do not already have a path.info file or min.data.info files from OPTIM. If you do have these files, then you can use STARTFROMPATH for a path.info file, or ADDMIN if you have min.data.info.

==== A. Potentials that DO NOT use start files ====
'''Step 1.''' First generate '''min.data.info.1''' for endpoint 1: 

<code> ~/svn/OPTIM/builds/ifort_64_2019_5_281/OPTIM 1 </code>

'''Note:''' the extension '''1''' refers to the file odata.1 that must be present in the directory. 

'''Step 2.''' Then, generate similarly for endpoint 2: 

<code> ~/svn/OPTIM/builds/ifort_64_2019_5_281/OPTIM 2 </code>

'''Note:''' the extension '''2''' refers to the file odata.2 that must be present in the directory.

The '''odata.1''' and '''odata.2''' files must contain OPTIM minimisation commands + DUMPDATA and ENDHESS commands to generate the min.data.info.* files. For example, an odata.1 file (that uses the xtb potential) could be of the form:

'''odata.1:'''

XTB C24xtb '--acc 0.1 --gfn2 -P 8' 
UPDATES 100 100 
BFGSCONV 1.0D-5 
BFGSMIN 1.0D-5 
CONVERGE 1.0D-5 
BFGSSTEPS 60000 
DEBUG 

DUMPDATA 
ENDHESS 

MAXERISE 1.0D-4 1.0D0

DUMPALLPATHS 
STEPS 400 

POINTS 
C -2.04053148527331 1.05306390371634 -0.253877546750764E-11 
C -1.05306390370855 0.172720191240289E-11 -2.04053148528364 
C -0.546121488999475E-12 2.04053148529656 -1.05306390369997 
C -0.146298180312409E-11 2.04053148530069 1.05306390369198 
C -0.914160192067804E-12 -2.04053148529553 -1.05306390370031 
C -0.287393036865366E-11 -2.04053148530158 1.05306390369083 
C -2.04053148527466 -1.05306390371639 -0.367973225662900E-11 
C 2.04053148526781 -1.05306390372175 -0.875778282666703E-12 
C -1.05306390372231 -0.979254867490875E-12 2.04053148526605 
C 2.04053148527107 1.05306390372396 -0.182101538055068E-11 
C 1.05306390370932 -0.340215830916567E-12 2.04053148528387 
C 1.05306390370268 0.258658422685307E-13 -2.04053148528689 
C 0.710799972739704E-12 1.05306390368809 -2.04053148527393 
C 1.05306390371174 -2.04053148526187 0.955967560634191E-12 
C -2.04053148525347 0.881144607755502E-13 1.05306390371966 
C 0.344943596544608E-11 1.05306390367851 2.04053148528088 
C 2.04053148526428 0.762070953548885E-12 1.05306390369870 
C 2.04053148526827 0.865526145990094E-13 -1.05306390369420 
C -2.04053148526448 0.713448152766709E-12 -1.05306390370007 
C -1.05306390370763 2.04053148526678 0.446469677757191E-11 
C 1.05306390371344 2.04053148526008 0.938221027950337E-13 
C 0.419813438210074E-11 -1.05306390367943 2.04053148528005 
C -1.05306390370769 -2.04053148526729 0.524101153866833E-11 
C 0.938323209745303E-12 -1.05306390368924 -2.04053148527485 

'''Step 3.''' Once the two '''min.data.info.1''' and '''min.data.info.2''' files are generated, they are copied to the pathsample directory where they are then combined into one file 

<code>cat min.data.info.1 min.data.info.2 > min.data.info</code> 

'''Step 4.''' The combined file is read with the READMIN command in pathdata and then PATHSAMPLE generates the database files '''min.data''' and '''points.min''' from which a DIJINITSTART/CONNECTREGION/DIJINITCONT job can be launched. For the above purpose, a pathdata file (that uses the xtb potential) could be of the form:

'''pathdata:'''

GCORES '-c8' 
SYSTEM X 
EXEC ~/svn/OPTIM/builds/ifort_64_2019_5_281/OPTIM 
NATOMS 24 
SEED 1 
DIRECTION AB 
CONNECTIONS 1 
TEMPERATURE 0.592 
PLANCK 9.536D-14 

READMIN min.data.info 

'''Note:''' Before the next step, we should manually create '''min.A''' and '''min.B''' files to designate the indices of the endpoints.

'''Step 5.''' Finally, to launch the initial connection attempt with PATHSAMPLE the following '''pathdata''' and '''odata.connect''' files can be used (xtb potential): 

'''pathdata:'''

GCORES '-c8' 
SYSTEM X 
EXEC ~/svn/OPTIM/builds/ifort_64_2019_5_281/OPTIM 
NATOMS 24 
SEED 1 
DIRECTION AB 
CONNECTIONS 1 
TEMPERATURE 0.592 
PLANCK 9.536D-14 

! PERMDIST 

EDIFFTOL 1.0D-4 
GEOMDIFFTOL 0.3D0 

SLURM 
! CPUS 10 

! READMIN min.data.info 

PAIRLIST 1 
DIJINITCONT exp 
INITIALDISTANCE -1.0 
CYCLES 10 

! CONNECTREGION 13 11 5.0D0 
! CYCLES 10 

COPYFILES mass 
COPYOPTIM 

'''odata.connect:'''

XTB C24xtb '--acc 0.1 --gfn2 -P 8' 
! DEBUG 
NEWCONNECT 1 1 2.0 25.0 10 1.0 0.001 
NEWNEB 30 500 0.0001 
NEBK 100.0 

DIJKSTRA EXP 
! PERMDIST 

EDIFFTOL 1.0D-4 
GEOMDIFFTOL 0.3D0 

BFGSMIN 1.0D-6 
UPDATES 100 100 50 4 
PUSHOPT 0.1 0.001 100 
REOPTIMISEENDPOINTS 
BFGSSTEPS 2000 
MAXBFGS 0.3 0.3 
STEPS 1000 
RADIUS 999999.9 

! comment Perform a hybrid EF/LBFGS transition state search 
BFGSTS 2000 20 100 0.0001 
! CHECKNEGATIVE 
! ENDHESS 
NOHESS 
MAXTSENERGY 10.0D0 
MAXSTEP 0.1 
MAXMAX 0.3 
TRAD 0.2 
USEDIAG 2 
PATH 100 0.0001 

MAXERISE 1.0D-3 2.0D0 
DUMPALLPATHS 
DUMPSTRUCTURES 
POINTS 

====B. Potentials that use start files ====

'''Step 1.''' A file called '''start.1''' should contain the xyz coordinates of min1. Another file '''start.1.1''' should be a copy of start.1 

'''Step 2.''' A file called '''start.2''' should contain the xyz coordinates of min2. Another file '''start.2.2''' should be a copy of start.2 

'''Note:''' the atomic symbols/masses should also be passed to PATHSAMPLE/OPTIM and this is done differently for each potential. Refer to potential-specific documentation.

<nowiki>For example:</nowiki>

In ''Tapered ReaxFF'', the elements are passed from '''fort.3''' file that must be present. The masses are encoded internaly per-element in the code, so no need to pass them.

In ''DFTBP'', the elements are passed from the '''dftb_in.hsd''' file that must be present. The masses are encoded internaly per-element in the code, so no need to pass them.

In ''xtb'', the elements and masses are passed from '''mass''' file that must be present. 

'''Step 3.''' odata.start and odata.finish should contain OPTIM minimisation commands for min1 and min2, respectively. For example, an odata.start file (that uses the DFTBP potential) could be of the form:

'''odata.start:'''

UPDATES 100 100 
BFGSCONV 1.0D-6 
BFGSMIN 1.0D-6 
CONVERGE 1.0D-6 
BFGSSTEPS 60000 
DEBUG 
DUMPDATA 
ENDHESS 
MAXERISE 1.0D-4 1.0D0 
DUMPALLPATHS 
STEPS 400 
DFTBP start 

'''Step 4.''' odata.connect should contain the OPTIM connection commands. For example, an odata.connect file (that uses the DFTBP potential) could be of the form:

'''odata.connect'''

! DEBUG
NEWCONNECT 1 1 2.0 25.0 10 1.0 0.001 
NEWNEB 30 500 0.0001 
NEBK 100.0 

DIJKSTRA EXP 
! PERMDIST 

EDIFFTOL 1.0D-4 
GEOMDIFFTOL 0.3D0 

BFGSMIN 1.0D-6 
UPDATES 100 100 50 4 
PUSHOPT 0.1 0.001 100 
REOPTIMISEENDPOINTS 
BFGSSTEPS 2000 
MAXBFGS 0.3 0.3 
STEPS 1000 
RADIUS 999999.9 

! comment Perform a hybrid EF/LBFGS transition state search 
BFGSTS 2000 20 100 0.0001 
! CHECKNEGATIVE 
! ENDHESS 
NOHESS 
MAXTSENERGY 10.0D0 
MAXSTEP 0.1 
MAXMAX 0.3 
TRAD 0.2 
USEDIAG 2 
PATH 100 0.0001 

MAXERISE 1.0D-3 2.0D0 
DUMPALLPATHS 
DUMPSTRUCTURES 
DFTBP start 

'''Step 5.''' pathdata file should contain the DIJINITSTART keyword to start an initial connection job and produce the database files (min.data, ts.data, points.min and points.ts). 

For example, an odata.connect file (that uses the DFTBP potential) could be of the form:

'''odata.connect:'''

EXEC ~/svn/OPTIM/builds/ifort_64_2019_5_281/DFTBPOPTIM 
NATOMS 32 
SEED 1 
DIRECTION AB 
CONNECTIONS 1 
TEMPERATURE 0.592 
PLANCK 9.536D-14 

! PERMDIST 
! LPERMDIST 3 0.2 6.0 0.001 
! RANROT 1600 

EDIFFTOL 1.0D-4 
GEOMDIFFTOL 0.3D0 

SLURM 
! CPUS 10 

DIJINITSTART exp 
INITIALDISTANCE -1.0 
CYCLES 1 

! PAIRLIST 1 
! DIJINITCONT exp 
! INITIALDISTANCE -1.0 
! CYCLES 1 

! ADDMIN min.data.info 

! CONNECTREGION 13 11 5.0D0 
! CYCLES 10 

DFTBP 
COPYFILES *.skf dftb_in.hsd 
COPYOPTIM 

'''Note:''' after a few connections have been made already (and with the databse present), it is possible to stop the job, and replace DIJINISTART with DIJINITCONT, which will continue the connection attempts and add new stationary points to the database.

STARTING INITIAL PATH JOBS WITH PATHSAMPLE - Revision history

Df398 at 10:45, 17 November 2020

Df398: This page describes how to perform initial connection jobs with PATHSAMPLE (assuming no path.info or min.data.info files are present)