11. Appendix

11.1. ProteinDF startup options

  • -r

Restarts computation from available points. The calculation conditions are loaded from the parameter file (pdfparam.mpac).

  • -i input_file

Starts computation with a specified input file. If not specified, the fl_Userinput file in the current directory is used.

  • -o output_file

Outputs debug logs. A large number of messages may be output in the output file and standard output. Normally it is not necessary to use this option.

  • -d

Specifies the output file for the results. If not specified, the fl_Out_Std file is output in the current directory.

11.2. Input parameter list

  • pdf_param_path

Parameter

pdf_param_path

Description

Specifies the path of the ProteinDF parameter file.

Default

pdfparam.mpac

Values

.*
  • step_control

Parameter

step_control

Description

Specifies the calculation scheme.

Default

create

Values

((create|integral|guess|scf|force)s*)+
  • comment

Parameter

comment

Description

comment

Default

 

Values

.*
  • linear_algebra_package

Parameter

linear_algebra_package

Description

Specifies the linear operation library.

Default

lapack

Values

(lapack|scalapack)
  • scalapack_block_size

Parameter

scalapack_block_size

Description

Specifies the block size of the ScaLAPACK library.

Default

64

Values

(d+)
  • save_distributed_matrix_to_local_disk

Parameter

save_distributed_matrix_to_local_disk

Description

Saves distributed matrix to each node local disk (yes).

Default

no

Values

(yes|no)
  • local_disk_path

Parameter

local_disk_path

Description

Specifies the local disk directory in which to save distributed matrix.

Default

/tmp

Values

.*
  • memory_size

Parameter

memory_size

Description

Specifies the memory size available for computation.

Default

1GB

Values

d+s*(MB|GB)
  • use_mapfile

Parameter

use_mapfile

Description

Uses memory-mapped files (yes).

Default

no

Values

(yes|no)
  • mapfile_size

Parameter

mapfile_size

Description

Specifies the size of the memory- mapped file.

Default

auto

Values

(d+s*(MB|GB)|auto)
  • mapfile_basename

Parameter

mapfile_basename

Description

Specifies the path of the memory-mapped file.

Default

pdf

Values

.*
  • work_on_disk

Parameter

work_on_disk

Description

Forcefully uses memory-mapped files (yes).

Default

no

Values

(yes|no)
  • parallel_processing_type

Parameter

parallel_processing_type

Description

Selects the parallel computation algorithm.

Default

divide_and_conquer

Values

(divide_and_conquer|DC|master_slave|MS)
  • cleanup

Parameter

cleanup

Description

Deletes intermediate files (yes).

Default

no

Values

(yes|no)
  • show_keyword

Parameter

show_keyword

Description

Outputs the ProteinDF parameters (yes).

Default

no

Values

(yes|no)
  • show_input

Parameter

show_input

Description

Outputs the ProteinDF parameters specified with input files (yes).

Default

yes

Values

(yes|no)
  • show_coordinates

Parameter

show_coordinates

Description

Outputs the molecular coordinates (yes).

Default

yes

Values

(yes|no)
  • show_orbital_basis

Parameter

show_orbital_basis

Description

Outputs the current basis sets in the specified format.

Default

gamess

Values

(gamess|amoss|none)
  • guess

Parameter

guess

Description

Specifies the initial guess for SCF loop.

Default

rho

Values

(rho|file_rho|lcao|density|core|huckel|harris)
  • cut-value

Parameter

cut-value

Description

Specifies the cut off value for molecular integrals.

Default

1.0E-10

Values

(double > 0)
  • block-size

Parameter

block-size

Description

Specifies the block size for molecular integrals.

Default

1024000

Values

(integer > 0)
  • charge-extrapolate-number

Parameter

charge-extrapolate-number

Description

Specifies the SCF iteration number to start extrapolating the charge (X).

Default

1

Values

(integer >= 1)
  • orbital-overlap-correspondence

Parameter

orbital-overlap-correspondence

Description

Uses the orbital overlap method when obtaining density matrices (yes).

Default

off

Values

on/off
  • orbital-overlap-correspondence-first

Parameter

orbital-overlap-correspondence-first

Description

Specifies whether or not to use the orbital-overlap-correspondence method or mo-projection method from the first SCF iteration. Only valid when the initial guess is LCAO.

Default

off

Values

on/off
  • orbital-overlap-correspondence-method

Parameter

orbital-overlap-correspondence-method

Description

Specifies whether to use the orbital-overlap-correspondence method, or mo-projection method.

Default

mo-overlap

Values

mo-overlap/mo-projection
  • orbital-overlap-correspondence-number

Parameter

orbital-overlap-correspondence-number

Description

 

Default

3

Values

integer
  • summary

Parameter

summary

Description

Outputs the summary of computation. A large amount of data may be output depending on the calculation scale.

Default

none

Values

(none|convergence|every-scf)
  • analyze_population

Parameter

analyze_population

Description

Outputs the formal charge. A large amount of data may be output depending on the calculation scale.

Default

none

Values

(none|convergence|every-scf)
  • max-iteration

Parameter

max-iteration

Description

Specifies the maximum number of SCF iterations.

Default

100

Values

(integer)
  • method

Parameter

method

Description

Specifies the spin handling method.

Default

rks

Values

(rks|uks|roks)
  • method/rks/occlevel

Parameter

method/rks/occlevel

Description

Specifies the level of occupied orbitals.

Default

 

Values

(array of integer >= 0)
  • method/rks/electrons

Parameter

method/rks/electrons

Description

Specifies the electron count.

Default

 

Values

(integer >= 2)
  • method/uks/alpha_occlevel

Parameter

method/uks/alpha_occlevel

Description

Specifies the alpha-spin occupied orbitals.

Default

 

Values

(array of integer >= 0)
  • method/uks/alpha_electrons

Parameter

method/uks/alpha_electrons

Description

Specifies the alpha spin electron count.

Default

 

Values

(integer >= 1)
  • method/uks/beta_occlevel

Parameter

method/uks/beta_occlevel

Description

Specifies the beta-spin occupied orbitals.

Default

 

Values

(array of integer >= 0)
  • method/uks/beta_electrons

Parameter

method/uks/beta_electrons

Description

Specifies the beta spin electron count.

Default

 

Values

(integer >= 1)
  • method/roks/closed_occlevel

Parameter

method/roks/closed_occlevel

Description

roks計算における閉殻軌道の指定

Default

 

Values

(array of integer >= 1)
  • method/uks/close_electrons

Parameter

method/uks/close_electrons

Description

roks計算における閉殻軌道の電子数

Default

 

Values

(array of integer >= 0)
  • method/roks/open_occlevel

Parameter

method/roks/open_occlevel

Description

roks計算における開殻軌道の指定

Default

 

Values

(array of integer >= 1)
  • method/uks/beta_occlevel

Parameter

method/uks/beta_occlevel

Description

Specifies the beta-spin occupied orbitals.

Default

 

Values

(array of integer >= 0)
  • save_diff_density_matrix

Parameter

save_diff_density_matrix

Description

 

Default

yes

Values

(yes|no)
  • use_matrix_cache

Parameter

use_matrix_cache

Description

 

Default

yes

Values

(yes|no)
  • force_loading_from_disk

Parameter

force_loading_from_disk

Description

 

Default

yes

Values

(yes|no)
  • show_cache_report

Parameter

show_cache_report

Description

Reports the memory cash usage.

Default

no

Values

(yes|no)
  • disk-utilization

Parameter

disk-utilization

Description

 

Default

no

Values

yes/no
  • update_method

Parameter

update_method

Description

 

Default

yes

Values

(yes|no)
  • orbital-independence-threshold

Parameter

orbital-independence-threshold

Description

 

Default

0.007

Values

(real >= 0)
  • convergence/type

Parameter

convergence/type

Description

Specifies the convergence judgment parameters.

Default

density

Values

(fock|density|dcoef)
  • convergence/threshold

Parameter

convergence/threshold

Description

Specifies the convergence judgment threshold.

Default

1e-3

Values

(real > 0)
  • convergence/threshold-energy

Parameter

convergence/threshold-energy

Description

Specifies the energy threshold for convergence judgment.

Default

1e-4

Values

(real > 0)
  • scf-acceleration

Parameter

scf-acceleration

Description

Specifies the convergence acceleration method.

Default

damping

Values

(damping|anderson|diis)
  • scf-acceleration/damping/damping-factor

Parameter

scf-acceleration/damping/damping-factor

Description

Specifies the factor of the damping method.

Default

0.85

Values

(real)
  • scf-acceleration/daming/start-number

Parameter

scf-acceleration/daming/start-number

Description

Specifies the number of SCF iteration to start the damping method.

Default

0

Values

(int)
  • scf-acceleration/damping/damping-type

Parameter

scf-acceleration/damping/damping-type

Description

Specifies the parameters to which to apply the damping method.

Default

density

Values

(fock|density_matrix|density|dcoef)
  • scf-acceleration/anderson/damping-factor

Parameter

scf-acceleration/anderson/damping-factor

Description

Specifies the damping factor for Anderson’s method.

Default

0.50

Values

(real)
  • scf-acceleration/anderson/start-number

Parameter

scf-acceleration/anderson/start-number

Description

Specifies the number of SCF iteration to start the Anderson’s method.

Default

3

Values

(int)
  • level-shift

Parameter

level-shift

Description

Applies the level shift method.

Default

no

Values

(yes|no)
  • level-shift/start-iteration

Parameter

level-shift/start-iteration

Description

Specifies the number of SCF iteration to start the level shift method.

Default

1

Values

(int)
  • level-shift/ls-closed-mo

Parameter

level-shift/ls-closed-mo

Description

Specifies the shift value applied to closed orbitals in the level shift method.

Default

0.00

Values

(real)
  • level-shift/ls-open-mo

Parameter

level-shift/ls-open-mo

Description

Specifies the shift value applied to open orbitals in the level shift method.

Default

0.00

Values

(real)
  • level-shift/ls-virtual-mo

Parameter

level-shift/ls-virtual-mo

Description

Specifies the shift value applied to unoccupied orbitals in the level shift method.

Default

0.00

Values

(real)
  • scf-acceleration/diis/number-of-diis

Parameter

scf-acceleration/diis/number-of-diis

Description

 

Default

3

Values

(integer)
  • scf-acceleration/diis/start-number

Parameter

scf-acceleration/diis/start-number

Description

Specifies the number of vectors referred in the DIIS method.

Default

3

Values

(integer >= 0)
  • scf-acceleration/diis/start-extrapolation

Parameter

scf-acceleration/diis/start-extrapolation

Description

 

Default

6

Values

(integer >= 0)
  • xc-potential

Parameter

xc-potential

Description

Specifies the exchange-correlation functional.

Default

svwn~

Values

(svwn~|svwn|blyp|b3lyp)
  • grid_free

Parameter

grid_free

Description

use grid-free method.

Default

false

Values

(yes|no)
  • xc-potential/grid-type

Parameter

xc-potential/grid-type

Description

Specifies the threshold of the electron density at the grid point.

Default

sg-1

Values

fine/medium-fine/medium/coarse/sg-1
  • xc-update

Parameter

xc-update

Description

 

Default

yes

Values

(yes|no)
  • xc-density-threshold

Parameter

xc-density-threshold

Description

 

Default

1.0E-16

Values

real
  • TEI-integral-driven

Parameter

TEI-integral-driven

Description

 

Default

yes

Values

(yes|no)
  • J_engine

Parameter

J_engine

Description

Specifies the calculation engine for the Coulomb term.

Default

RI_J

Values

(conventional|RI_J|CD)
  • K_engine

Parameter

K_engine

Description

Specifies the calculation engine for the Fock exchange term.

Default

conventional

Values

(conventional|RI_K|CD)
  • CDAM_tau

Parameter

CDAM_tau

Description

Specifies the threshold of pre-screening in the CD method.

Default

1.0E-10

Values

(real)
  • CD_epsilon

Parameter

CD_epsilon

Description

Specifies the threshold of the error tolerance in the CD method.

Default

1.0E-4

Values

(real)
  • scf-memory-saving

Parameter

scf-memory-saving

Description

 

Default

no

Values

yes/no
  • geometry/cartesian/input

Parameter

geometry/cartesian/input

Description

Specifies molecular structure in the Cartesian coordinate system.

Default

nil

Values

nil/stored
  • geometry/cartesian/unit

Parameter

geometry/cartesian/unit

Description

 

Default

a.u.

Values

au/a.u./angstrom
  • basis-set/orbital

Parameter

basis-set/orbital

Description

 

Default

nil

Values

nil/stored
  • basis-set/density-auxiliary

Parameter

basis-set/density-auxiliary

Description

 

Default

nil

Values

nil/stored
  • basis-set/exchange-auxiliary

Parameter

basis-set/exchange-auxiliary

Description

 

Default

nil

Values

nil/stored
  • xc_density_threshold

Parameter

xc_density_threshold

Description

 

Default

1.0E-16

Values

real
  • geometry

Parameter

geometry

Description

 

Default

cartesian

Values

cartesian/file
  • coordinates

Parameter

coordinates

Description

 

Default

 

Values

 
  • basis_sets

Parameter

basis_sets

Description

 

Default

 

Values

 
  • basis_sets_j

Parameter

basis_sets_j

Description

 

Default

 

Values

 
  • basis_sets_k

Parameter

basis_sets_k

Description

 

Default

 

Values

 
  • independent-orbital-number

Parameter

independent-orbital-number

Description

 

Default

0

Values

(integer > 0)
  • xc-potential/gxalpha/alpha-value

Parameter

xc-potential/gxalpha/alpha-value

Description

 

Default

0.7

Values

real
  • myu-nyu-zero

Parameter

myu-nyu-zero

Description

 

Default

no

Values

(yes|no)
  • guess/nsp-ppq

Parameter

guess/nsp-ppq

Description

 

Default

nil

Values

nil/stored
  • guess/sp-ppq

Parameter

guess/sp-ppq

Description

 

Default

nil

Values

nil/stored
  • guess/trans-angle-threshold

Parameter

guess/trans-angle-threshold

Description

 

Default

1.0 1.5 20 30

Values

nil/stored
  • guess/make-myu-nyu

Parameter

guess/make-myu-nyu

Description

 

Default

meth0

Values

meth0/meth1/meth2/meth3/meth4
  • guess/vct-normalize

Parameter

guess/vct-normalize

Description

 

Default

ON OFF OFF

Values

 
  • guess/part-normalize

Parameter

guess/part-normalize

Description

 

Default

nil

Values

nil/stored
  • guess/user-vector

Parameter

guess/user-vector

Description

 

Default

nil

Values

(nil|stored)
  • num_of_atoms

Parameter

num_of_atoms

Description

 

Default

 

Values

 
  • num_of_dummy_atoms

Parameter

num_of_dummy_atoms

Description

 

Default

 

Values

 
  • num_of_AOs

Parameter

num_of_AOs

Description

 

Default

 

Values

 
  • num_of_MOs

Parameter

num_of_MOs

Description

 

Default

 

Values

 
  • num_of_auxCDs

Parameter

num_of_auxCDs

Description

 

Default

 

Values

 
  • num_of_auxXCs

Parameter

num_of_auxXCs

Description

 

Default

 

Values

 
  • TE

Parameter

TE

Description

 

Default

 

Values

 
  • debug/file_warning

Parameter

debug/file_warning

Description

 

Default

yes

Values

(yes|no)
  • debug/save_J

Parameter

debug/save_J

Description

 

Default

no

Values

(yes|no)
  • debug/save_K

Parameter

debug/save_K

Description

 

Default

no

Values

(yes|no)
  • debug/save_Fxc_pure

Parameter

debug/save_Fxc_pure

Description

 

Default

no

Values

(yes|no)
  • debug/save_forces

Parameter

debug/save_forces

Description

 

Default

no

Values

(yes|no)
  • cutoff_distribution

Parameter

cutoff_distribution

Description

 

Default

 

Values

 
  • length_scale_parameter

Parameter

length_scale_parameter

Description

 

Default

1

Values

 
  • control

Parameter

control

Description

 

Default

 

Values

 
  • debug/eri/exact_J

Parameter

debug/eri/exact_J

Description

 

Default

 

Values

 
  • cutoff_density

Parameter

cutoff_density

Description

 

Default

 

Values

 
  • cutoff_epsilon3

Parameter

cutoff_epsilon3

Description

 

Default

 

Values

 
  • debug/eri/exact_K

Parameter

debug/eri/exact_K

Description

 

Default

 

Values

 
  • new_engine

Parameter

new_engine

Description

 

Default

 

Values

 
  • debug/eri/output_K

Parameter

debug/eri/output_K

Description

 

Default

 

Values

 
  • debug/eri/output_J

Parameter

debug/eri/output_J

Description

 

Default

 

Values

 
  • num_of_iterations

Parameter

num_of_iterations

Description

 

Default

 

Values

 
  • stat

Parameter

stat

Description

 

Default

 

Values

 

11.3. Input file format

11.4. basis2 file format

The basis2 file stores the basis set data. The following shows a sample of the file:

O-DZVP2.C
    3 2 1
    7
       5784.15710000	      0.00081900
        869.30350000	      0.00629350
        198.51164000	      0.03178120
         56.42990100	      0.11727340
         18.28545700	      0.30347630
          6.44871460	      0.45352140
          2.34185960	      0.24305910
    2
          5.45953280	     -0.07780440
          0.47819680	      0.57149470
    1
          0.14573010	      1.00000000
    5
         34.25856300	      0.00580430
          7.86389540	      0.04064030
          2.34451930	      0.15502190
          0.79617150	      0.35314440
          0.27268040	      0.45500620
    1
          0.08926050	      1.00000000
    1
          0.60000000	      1.00000000
  • Format

** 1st line (title line)

Describe the basis set name. The names beginning with O- and A- signify basis sets and auxiliary basis sets, respectively. The basis set name consists of a single CGTO block. The auxiliary basis set name consists of two CGTO blocks, representing the auxiliary basis sets for the Coulomb term and exchange-correlation term.

** 2nd line (CGTO block start line)

Specify the type and number of the orbitals of contracted Gaussian-type basis sets (CGTO). The three integers separated with a blank character represent the number of s-types, p-types, and d-types, respectively. A CGTO block follows this line.

“3 2 1”と記述されていた場合、 s型の縮約ガウス型基底関数が3つ、 p型の縮約ガウス型基底関数が2つ、 d型の縮約ガウス型基底関数が1つ含まれていることを表します。 したがって、この行以降、7つのCGTOブロックが記述されることになります。

** 3rd line (CGTO start line)

The number at the top of a CGTO block signifies the number of primitive Gaussian-type basis sets (PGTO) contained in the current block.

** 4th line (PGTO line)

Describe the exponent and coefficient of the primitive Gaussian-type basis set (PGTO) by separating them with a blank character. The coefficient (1.0) can be omitted for auxiliary basis sets.

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