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.