orthomol.x

Description

orthomol is a TurboRVB utility that orthogonalizes selected molecular orbitals in a fort.10 wave function on a real-space mesh and writes the result to fort.10_new.

• Input: fort.10 (wave function containing molecular orbitals), standard input with namelists &mesh_info (mesh nx, ny, nz, ax, ay, az, etc.) and &molec_info (nummol and the list of orbital indices wheremol). If pseudopotentials are used, pseudo.dat is read.

• Output: fort.10_new — same structure as fort.10, with the specified molecular orbitals orthogonalized by ortho_fast (convertmod). Written by rank 0 only; written with contraction=1.

• The program reads fort.10 via read_fort10_fast, read_pseudo, read_fort10(10), then calls ortho_fast to orthogonalize the selected orbitals on the mesh (overlap-based) and writes the result with write_fort10(10).

• Typical use: After convertfort10mol or similar, when the molecular orbitals in fort.10 are not orthogonal; use orthomol to orthogonalize the chosen orbitals before VMC/DMC.

The program supports MPI (when built with PARALLEL): rank 0 performs file I/O and reads namelists from stdin, then broadcasts mesh and orbital list to other ranks. Run with --help, -help, or help to show online help (help_online('orthomol')) and exit.

Input and output

Input

• fort.10 (required): Wave function file (TurboRVB format) to be orthogonalized. Opened by rank 0 on unit 10; read via read_fort10_fast, read_pseudo, read_fort10(10). Must contain molecular orbitals (molecular).

• Standard input: Namelist &mesh_info (nbufd, nx, ny, nz, ax, ay, az, shift_origin, shiftx, shifty, shiftz). Then &molec_info (nummol). If nummol ≠ 0, the next line must list wheremol(1:abs(nummol)) as integers. See template/orthomol.input for an example.

• pseudo.dat: Required when pseudopotentials are used (npsa > 0); read by read_pseudo.

• Command line: First argument --help, -help, or help prints online help and exits.

nummol and wheremol

• nummol > 0: wheremol(1:nummol) are absolute orbital indices (range nelorb_c - molecular + 1 to nelorb_c). Give them on one line after &molec_info.

• nummol < 0: wheremol(1:abs(nummol)) are relative indices (1 to molecular). The program converts them to absolute indices internally (wheremol(i) = wheremol(i) + nelorb_c - molecular).

• nummol = 0: Program prints "Nothing to be orthogonalized" and exits without writing fort.10_new.

Output

• fort.10_new: Wave function with the selected molecular orbitals orthogonalized. Same format and structure as fort.10; written with contraction=1 via write_fort10(10). Written by rank 0 only. Overwrites existing file.

Input parameters

Variable are read from standard input.

mesh_info section

Parameter name	Datatype	Default	Description
nbufd	integer	if no input 1000 if nelorb < 2000 100 if nelorb >= 2000	WIP
nx	integer	error if no input	WIP
ny	integer	nx	WIP
nz	integer	ny	WIP
ax	real*8	if no input 0.1d0 if iespbc is .false. ignore input cellscale(1)/nx if iespbc is .true.	WIP
ay	real*8	if no input ax if iespbc is .false. ignore input cellscale(2)/ny if iespbc is .true.	WIP
az	real*8	if no input ay if iespbc is .false. ignore input cellscale(3)/nz if iespbc is .true.	WIP
shift_origin	logical	.true.	WIP
shiftx	logical	.false.	WIP
shifty	logical	.false.	WIP
shiftz	logical	.false.	WIP

molec_info section

Parameter name	Datatype	Default	Description
nummol	integer	error if no input	WIP

wheremol

Parameter name	Datatype	Default	Description
wehremol	integer, allocatable, dimension(:) :: wheremol	read wheremol(1:nummol) if nummol > 0 wheremol(1:abs(nummol)) = nelorb_c - molecular if nummol < 0	WIP

Notes

MPI (parallel runs)

• orthomol is built with MPI support when PARALLEL is defined. Run with mpirun -np N ./orthomol.x < input (or equivalent). Rank 0 opens fort.10, reads stdin (namelists and wheremol line), and writes fort.10_new; mesh and molec_info / wheremol are broadcast to all ranks. ortho_fast is executed by all ranks.

• Ensure fort.10 and (if used) pseudo.dat are visible to the process running as rank 0 (e.g. shared working directory).

Mesh and defaults

• nx must be positive; if nx=0 after reading &mesh_info, the program stops with "The number of mesh point is zero !!!". Defaults: nx=ny=nz=0, so you must set at least nx in &mesh_info (e.g. nx=20). If ny=0, it is set to nx; if nz=0, to ny.

• For periodic boundary conditions (iespbc), ax, ay, az are overwritten from the cell: ax = cellscale(1)/nx, etc.

• nbufd default: 1000 if nelorb < 2000, else 100.

Pseudopotentials

• If fort.10 has pseudopotential data (npsa > 0), pseudo.dat must be present in the working directory; it is read by read_pseudo.

Related programs

• convertfort10mol: Converts the molecular-orbital part of fort.10 to another basis. Use orthomol afterward to orthogonalize those orbitals in fort.10_new.

• convertmod: Provides the ortho_fast subroutine used for overlap-based orthogonalization on the mesh.

• read_fort10 / write_fort10: Fort.10 read/write routines; orthomol uses them for fort.10 and fort.10_new.

• template/orthomol.input: Example standard input (&mesh_info, &molec_info, and one line of wheremol indices).

Troubleshooting

Fatal errors (program stops)

• The number of mesh point is zero !!! — nx is 0 (default or explicitly set in &mesh_info). Set a positive nx in &mesh_info (e.g. nx=20).

• Nothing to be orthogonalized — nummol is 0; no orbitals were selected for orthogonalization. Set nummol to a non-zero value (positive or negative) and provide the wheremol list on the next line.

• Cannot open fort.10 / read_fort10 fails — fort.10 missing or invalid format. Put a valid TurboRVB fort.10 (with molecular orbitals) in the working directory.

• read_pseudo fails — Pseudopotentials are used but pseudo.dat is missing or invalid. Provide pseudo.dat or use a fort.10 without ECPs.

Other notes

• fort.10_new is overwritten if it exists. Back it up if needed.

• wheremol indices: when using nummol > 0, use absolute indices in the range nelorb_c - molecular + 1 to nelorb_c; when using nummol < 0, use relative indices 1 to molecular.