Adding a model to OPTIM - Revision history

import>Jmc49 at 12:53, 4 February 2014

2014-02-04T12:53:00Z

← Older revision		Revision as of 12:53, 4 February 2014
Line 1:		Line 1:
	Adding a potential ~~into~~ the ~~optim~~ TS ~~sampling~~ program requires at least		Adding a potential to the OPTIM geometry optimization program requires at least
	coordinates, energies and gradients. ~~Hessian~~ can also be used in some		coordinates, energies and gradients. Hessians can also be used in some
	of the algorithms.		of the algorithms.

	The program must know the number of atoms of the system at the onset		The program must know the number of atoms of the system at the onset
	to allocate the correct amount of memory. This is a list of the minimum		to allocate the correct amount of memory. This is a list of the minimum
	number of routines you may need to change.		number of routines you may need to change/check.

	1. '''~~getparms~~.f''' starts the program opens input file odata, set NATOMS		1. '''getparams.f''' starts the program opens input file odata, set NATOMS

			1.5 '''OPTIM.F''' calls keywords. Be sure to edit OPTIM.F, which is preprocessed to give OPTIM.f at compile time.
	1.5 '''optim.f''' calls keyword

	2. '''key.f90''' module for keywords		2. '''key.f90''' data module for keywords

	3. '''keywords.f''' reads odata and ~~intilizes~~ energy functions		3. '''keywords.f''' reads odata and initializes energy functions/other stuff

	4. '''fetchz.f''' read structure for ~~CONNECT~~ runs ~~calls~~ pertable		4. '''fetchz.f''' read the "finish" structure for double-ended (NEWCONNECT) runs. Calls pertable

	5. '''pertable.f''' add model ID e.g (AM ATSYM) to symbol table, assigns atomic mass		5. '''pertable.f''' add model ID e.g (AM ATSYM) to symbol table, assigns atomic mass
Line 21:		Line 21:
	6. '''potential.f''' Main interface between OPTIM and external potential		6. '''potential.f''' Main interface between OPTIM and external potential

		⚫	8. '''geopt.f''' controls single-ended geometry optimizations. Produces min.data.info files for pathsample
	7. '''finailio.f''' output

⚫	8. '''geopt.f''' min.data.info files for pathsample

	first line		first line
Line 31:		Line 29:
	coordinates in X,Y,Z		coordinates in X,Y,Z

	9. '''CONNECT/ncutils.f90''' input path.info files for pathsample		9. '''CONNECT/ncutils.f90''' produces input path.info files for pathsample

	10. '''NEB/nnutils.f90''' in RWG subroutine for outputing the correct neb.xyz.<a>		10. '''NEB/nnutils.f90''' in RWG subroutine for outputing the correct neb.xyz.<a>

			11. '''minpermdist.f90''' optimally superimposes structure 2 onto structure 1 with respect to whichever are applicable of: overall translation, overall rotation and permutational isomerization. Check that it's doing the right thing for your system!

import>Jmc49 at 17:03, 17 March 2011

2011-03-17T17:03:54Z

← Older revision	Revision as of 17:03, 17 March 2011
Line 1:	Line 1:
		Adding a potential into the optim TS sampling program requires at least
		coordinates, energies and gradients. Hessian can also be used in some
		of the algorithms.

		The program must know the number of atoms of the system at the onset
		to allocate the correct amount of memory. This is a list of the minimum
		number of routines you may need to change.

		1. '''getparms.f''' starts the program opens input file odata, set NATOMS

		1.5 '''optim.f''' calls keyword

		2. '''key.f90''' module for keywords

		3. '''keywords.f''' reads odata and intilizes energy functions

		4. '''fetchz.f''' read structure for CONNECT runs calls pertable

		5. '''pertable.f''' add model ID e.g (AM ATSYM) to symbol table, assigns atomic mass

		6. '''potential.f''' Main interface between OPTIM and external potential

		7. '''finailio.f''' output

		8. '''geopt.f''' min.data.info files for pathsample

		first line

		energy, log product positive hessian eigen values, order point group, prime moments of inertia, order parameters (CHARMM)

		coordinates in X,Y,Z

		9. '''CONNECT/ncutils.f90''' input path.info files for pathsample

		10. '''NEB/nnutils.f90''' in RWG subroutine for outputing the correct neb.xyz.<a>


		--[[User:mp466\|mp466]] 15:28, 1 July 2008 (BST)

import>Jmc49: Removing all content from page

2011-03-14T16:54:58Z

Removing all content from page

← Older revision		Revision as of 16:54, 14 March 2011
Line 1:		Line 1:
	Adding a potential into the optim TS sampling program requires at least
	coordinates, energies and gradients. Hessian can also be used in some
	of the algorithms.

	The program must know the number of atoms of the system at the onset
	to allocate the correct amount of memory. This is a list of the minimum
	number of routines you may need to change.

	1. '''getparms.f''' starts the program opens input file odata, set NATOMS

	1.5 '''optim.f''' calls keyword

	2. '''key.f90''' module for keywords

	3. '''keywords.f''' reads odata and intilizes energy functions

	4. '''fetchz.f''' read structure for CONNECT runs calls pertable

	5. '''pertable.f''' add model ID e.g (AM ATSYM) to symbol table, assigns atomic mass

	6. '''potential.f''' Main interface between OPTIM and external potential

	7. '''finailio.f''' output

	8. '''geopt.f''' min.data.info files for pathsample

	first line

	energy, log product positive hessian eigen values, order point group, prime moments of inertia, order parameters (CHARMM)

	coordinates in X,Y,Z

	9. '''CONNECT/ncutils.f90''' input path.info files for pathsample

	10. '''NEB/nnutils.f90''' in RWG subroutine for outputing the correct neb.xyz.<a>


	--[[User:mp466\|mp466]] 15:28, 1 July 2008 (BST)

import>Jmc49: New page: Adding a potential into the optim TS sampling program requires at least coordinates, energies and gradients. Hessian can also be used in some of the algorithms. The program must know the...

2011-03-14T14:10:04Z

New page: Adding a potential into the optim TS sampling program requires at least coordinates, energies and gradients. Hessian can also be used in some of the algorithms. The program must know the...

New page

Adding a potential into the optim TS sampling program requires at least
coordinates, energies and gradients. Hessian can also be used in some
of the algorithms.

The program must know the number of atoms of the system at the onset
to allocate the correct amount of memory. This is a list of the minimum
number of routines you may need to change.

1. '''getparms.f''' starts the program opens input file odata, set NATOMS

1.5 '''optim.f''' calls keyword

2. '''key.f90''' module for keywords

3. '''keywords.f''' reads odata and intilizes energy functions

4. '''fetchz.f''' read structure for CONNECT runs calls pertable

5. '''pertable.f''' add model ID e.g (AM ATSYM) to symbol table, assigns atomic mass

6. '''potential.f''' Main interface between OPTIM and external potential

7. '''finailio.f''' output

8. '''geopt.f''' min.data.info files for pathsample

first line

energy, log product positive hessian eigen values, order point group, prime moments of inertia, order parameters (CHARMM)

coordinates in X,Y,Z

9. '''CONNECT/ncutils.f90''' input path.info files for pathsample

10. '''NEB/nnutils.f90''' in RWG subroutine for outputing the correct neb.xyz.<a>

--[[User:mp466|mp466]] 15:28, 1 July 2008 (BST)