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User_manual
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===========================
SMASH user's manual
version 3.0.0
===========================
******************
Important settings
******************
In general, the default stack size of system resources and the default
size of the OMP_STACKSIZE environmental variable are small.
Set new stack sizes according to your shell.
* bash:
Write the following two lines in the ~/.bashrc file.
ulimit -s unlimited
export OMP_STACKSIZE=1G
* csh, tcsh:
Write the following two lines in the ~/.cshrc or ~/.tcshrc file.
unlimit
setenv OMP_STACKSIZE 1G
If a large calculation stops at the first SCF iteration, increase the
size of OMP_STACKSIZE.
Sample input and output
-----------------------
Sample input and output files are included in the example directory.
How to run SMASH
----------------
* Intra-node (OpenMP) parallel computing
Set the OMP_NUM_THREADS environment variable to specify the number
of threads for one process.
bash: in the ~/.bashrc file
export OMP_NUM_THEADS=(# of threads)
csh, tcsh: in the ~/.cshrc or ~/.tcshrc file
setenv OMP_NUM_THEADS (# of threads)
After the setting, start a calculation.
$ bin/smash < input > output
or
$ bin/smash input output
or
$ bin/smash input
In the case of the last command, if the input file name is ***.inp or ***.sinp,
the output file name is set to ***.out or ***.sout.
If not, the output file is set to (input file).out.
* Inter-node (MPI) parallel computing
Use "mpirun" or "mpiexec" command to start a calculation, and specify
the number of MPI processes by -np option.
$ mpirun -np (# of processes) bin/smash < input > output
or
$ mpirun -np (# of processes) bin/smash input output
or
$ mpirun -np (# of processes) bin/smash input
* Hybrid parallel computing
Parallel computing with MPI and OpenMP when you use cluster or
supercomputer systems. It is recommended that the value of
OMP_NUM_THREADS be set equal to the number of CPU cores in a node.
e.g.) Shell: tcsh Machine: 10nodes, 8cores/node
Write the following line in the ~/.tcshrc file.
setenv OMP_NUM_THREADS 8
And then, run the MPI job.
$ mpirun -np 10 bin/smash < input > output
Input format
------------
1. Overview
Computational conditions are set in first several lines.
Subsequently, molecular data, basis and effective core potential (ECP)
functions are set.
2. Keywords
2.1 List of keyword Sections
Section Function
-------------------------------
job : Basic computational condition
control : Detailed computational condition
scf : Self-consistent field
opt : Geometry optimization
dft : Density functional theory
mp2 : MP2
geom : Molecular data (atom type, geometry)
basis : Basis function
ecp : Effective Core Potential
charge : Nuclear atomic charge
2.2 job keywords
runtype specifies the type of computation.
= energy Molecular energy (default)
= gradient Molecular energy and gradient
= opt Molecular geometry optimization
(optimize is a synonym for opt.)
method specifies the method of computation.
= HF Hartree-Fock (default)
= B3LYP B3LYP DFT with VWN3
= B3LYP5 B3LYP DFT with VWN5
= MP2 Second-order Moller-Plesset perturbation theory
basis specifies basis functions.
= STO-3G (default)
= gen Basis functions for each element are set in
"basis" section. See Section 2.7.
= 3-21G
= 6-31G
= 6-31G*
= 6-31G**
= 6-31+G
= 6-31+G*
= 6-31+G**
= 6-31++G
= 6-31++G*
= 6-31++G**
= 6-311G
= 6-311G*
= 6-311G**
= 6-311+G
= 6-311+G*
= 6-311+G**
= 6-311++G
= 6-311++G*
= 6-311++G**
= cc-pvdz
= cc-pvtz
= cc-pvqz
= d95v
= lanl2dz
mem specifies the memory size per process. (default: 8GB)
Supported units: B, KB, MB, GB, TB
(memory is a synonym for mem.)
charge specifies the total charge of the system. (default: 0.0)
The value does not include point charges set in Charge section.
multi specifies the spin multiplicity of the system.
= 1 Singlet (default)
= 2 Doublet
= 3,4,... Triplet, Quartet, ...
scftype specifies the type of the SCF wavefunction.
= RHF Restricted (closed-shell) Hartree-Fock (default)
= UHF Unrestricted (open-shell) Hartree-Fock
ecp specifies ECP functions.
= none ECP functions are not used. (default)
= Lanl2DZ Hay-Wadt ECP function
= gen ECP functions for each element are set in
"ecp" section. See Section 2.8.
ncore specifies the number of frozen core orbitals
in electron correlation calculations.
(default: calculated automatically)
nvfz specifies the number of frozen virtual orbitals
in electron correlation calculations.
(default: 0)
2.2 control keywords
precision controls computational precision.
If the following variables are set, they take precedence
over the precision setting.
= high cutint2=1.0E-12, dconv=5.0E-6, optconv=1.0E-5, threshrho=1.0E-6,
threshdfock=1.0E-5, threshdftao=1.0E-4, nrad=150, nleb=590
= medium cutint2=1.0E-11, dconv=5.0E-6, optconv=1.0E-4, threshrho=1.0E-5,
threshdfock=1.0E-4, threshdftao=1.0E-3, nrad=96, nleb=302 (default)
= low cutint2=1.0E-10, dconv=1.0E-5, optconv=1.0E-3, threshrho=1.0E-4,
threshdfock=1.0E-4, threshdftao=1.0E-2, nrad=72, nleb=302
spher specifies spherical harmonics or Cartesian basis functions.
= .true. Speherical harmonics (5d, 7f, 9g, 11h, 13i, default)
= .false. Cartesian (6d, 10f, 15g, 21h, 28i)
guess specifies the guess calculation.
= huckel extended Huckel calculation (default)
= check checkpoint file
check specifies the checkpoint file. (default: <empty>)
xyz specifies the xyz file. (default: <empty>)
cutint2 specifies the threshold for the two-electron integral calculation.
(default: 1.0E-11)
bohr specifies the unit of the input geometry.
= .false. Angstrom (default)
= .true. Atomic unit
print controls output format.
If iprint is set, it takes precedence over the print setting.
= minimum Minimum output without MO coefficients
= compact Compact output with MO coefficients of HOMO-9 to LUMO+9
= normal Normal output with MO coefficients of HOMO-9 to LUMO+9 (default)
= fullmo Normal output with all MO coefficients
= verbose Verbose output with all MO coefficients of all MOs
in every opt cycle
iprint controls output format.
Keyword "output" overrides "iprint" if both are set.
= 1 Minimum output without MO coefficients
= 2 Compact output with MO coefficients of HOMO-9 to LUMO+9
= 3 Normal output with MO coefficients of HOMO-9 to LUMO+9 (default)
= 4 Normal output with all MO coefficients
= 5 Verbose output with all MO coefficients of all MOs
in every opt cycle
threshover specifies the linear dependence threshold of basis functions.
(default : 1.0E-6)
threshatom specifies the atom distance threshold in Bohr.
(default : 2.0E-1)
pop specifies population (charge) calculations.
= mulliken Mulliken population (default)
= npa Natural Population Analysis (Natural Bond Orbital (NBO) charge)
+ Mulliken population (nbo is a synonym for npa.)
= none No population
multipole controls dipole, quadrupole, and octupole moment calculations.
= dipole Dipole only (default)
= octupole Dipole, quadrupole, and octupole
= none No multipole
2.3 scf keywords
scfconv specifies the type of SCF convergence method.
= DIIS Pulay's DIIS interpolation (default)
= SOSCF Approximate second-order SCF (SOSCF) method
= QC Quadratically convergent (QC) SCF method
maxiter specifies the maximum number of SCF iteration cycles.
(default: 150)
dconv specifies the SCF density convergence tolerance.
(default: 5.0E-6)
maxdiis specifies the maximum number of DIIS steps. (default: 20)
threshdiis specifies the threshold of DIIS start. (default: 6.0E-1)
maxsocf specifies the maximum number of SOSCF steps. (default: 20)
threshsoscf specifies the threshold of SOSCF start. (default: 2.5E-1)
maxqc specifies the maximum number of QC steps. (default: 15)
maxqcdiag specifies the maximum number of QC Davidson diagonalization.
(default: 100)
maxqcdiagsub specifies the maximum number of trial verctors of QC Davidson
diagonalization. (default: 10)
threshqc specifies the threshold of QC convergence. (default: 1.0E-5)
2.4 opt keywords
nopt specifies the maximum number of geometry optimization steps.
(default: 100)
optconv specifies the gradient convergence tolerance of geometry
optimization in Hartree/Bohr. (default: 1.0E-4)
RMS gradient tolerance is 1/3 of optonv.
cartesian specifies the type of the coordinate system.
= .false. Redundant coordinate (default)
= .true. Cartesian coordinate
fbond specifies the scaling factor of atom radii for
bond detection. (default: 1.20E+0)
2.5 dft keywords
nrad specifies the number of radial points. (default: 96)
nleb specifies the number of Lebedev angular points.
Possible values are 6, 14, 26, 38, 50, 86, 110,
146, 170, 194, 302, 350, 434, 590, 770, 974,
1202, and 1454. (default: 302)
threshweight specifies the threshold of the weight of a grid point.
(default: 1.0E-8)
threshrho specifies the threshold of the density of a grid point.
(default: 1.0E-5)
threshdfock specifies the threshold of the Fock matrix element of a grid point.
(default: 1.0E-4)
threshdftao specifies the threshold of the atomic orbital value of a grid point.
(default: 1.0E-3)
bqrad(9) specifies the radii of ghost atoms. (default: 1.06E+0)
2.6 mp2 keywords
maxmp2diis specifies the maximum number of DIIS iterations for CPHF of
MP2 energy gradient calculation. (default: 20)
maxmp2iter specifies the maximum number of iterations for CPHF of
MP2 energy gradient calculation. (default: 100)
threshmp2cphf specifies the CPHF convergence tolerance of
MP2 energy gradient calculation. (default: 1.0E-10)
2.7 geom
Write "geom" to specify the starting point for the molecular geometry.
After the line of "geom", write element symbols and their nuclear Cartesian
coordinates. A blank line or the end of the file means the end of the
molecular geometry section.
To read the molecular geometry of a checkpoint file, write "geom=check"
instead of "geom".
To use a dummy atom for a point charge, write "X" as an element symbol.
"Bq1"(=Bq) to "Bq9" are available as ghost atoms on which basis functions
and ECPs can be added for BSSE calculations.
e.g.) geom
O 0.0 0.0 0.0
H 1.0 0.0 0.0
H 0.0 1.0 0.0
X 0.0 0.0 3.0
2.8 basis
To use the basis section, basis=gen in the job section is necessary.
Write "basis" to specify the starting point for the basis functions.
After the line of "basis", write element symbols. From the next line,
write their basis set or basis functions. At the end of the basis set
or functions, write "****".
The format of basis functions is as follows.
(element symbols)
(angular momentum=S,P,D,F,G,H,ISP) (number of primitive functions)
(Gaussian exponent) (contraction coefficient) (P contraction coefficient if SP)
(Gaussian exponent) (contraction coefficient) (P contraction coefficient if SP)
...repeat the primitive function number of times
...repeat functions
****
A blank line or the end of the file means the end of the
basis function section.
e.g.1) C O
6-31G*
****
H
STO-3G
****
e.g.2) C
S 6
3047.5248800 0.0018347
457.3695180 0.0140373
103.9486850 0.0688426
29.2101553 0.2321844
9.2866630 0.4679413
3.1639270 0.3623120
SP 3
7.8682723 -0.1193324 0.0689991
1.8812885 -0.1608542 0.3164240
0.5442493 1.1434564 0.7443083
SP 1
0.1687145 1.0000000 1.0000000
D 1
0.8000000 1.0000000
****
H
S 3
18.7311370 0.0334946
2.8253944 0.2347270
0.6401217 0.8137573
S 1
0.1612778 1.0000000
****
2.9 ecp
To use the ecp section, ecp=gen in the job section is necessary.
Write "ecp" to specify the starting point for the ECP functions.
After the line of "basis", write element symbols. From the next line,
write their ECP function name or functions.
For ECP functions, the format is as follows.
(element symbols)
(name, anything OK) (maximum angular momentum) (number of removed core electrons)
(title, anything OK)
(number of Gaussians)
(power of R for Gaussian) (exponent of Gaussian) (coefficient of Gaussian)
(power of R for Gaussian) (exponent of Gaussian) (coefficient of Gaussian)
...repeat the Gaussian number of times
...repeat functions
A blank line or the end of the file means the end of the
ECP function section.
e.g.1) Fe Ru
LANL2DZ
e.g.2) Cl
Cl-ECP 2 10
d-ul potential
5
1 94.8130000 -10.0000000
2 165.6440000 66.2729170
2 30.8317000 -28.9685950
2 10.5841000 -12.8663370
2 3.7704000 -1.7102170
s-ul potential
5
0 128.8391000 3.0000000
1 120.3786000 12.8528510
2 63.5622000 275.6723980
2 18.0695000 115.6777120
2 3.8142000 35.0606090
p-ul potential
6
0 216.5263000 5.0000000
1 46.5723000 7.4794860
2 147.4685000 613.0320000
2 48.9869000 280.8006850
2 13.2096000 107.8788240
2 3.1831000 15.3439560
Br
Br-ECP 3 28
f-ul potential
4
1 213.6143969 -28.0000000
2 41.0585380 -134.9268852
2 8.7086530 -41.9271913
2 2.6074661 -5.9336420
s-ul potential
4
0 54.1980682 3.0000000
1 32.9053558 27.3430642
2 13.6744890 118.8028847
2 3.0341152 43.4354876
p-ul potential
5
0 54.2563340 5.0000000
1 26.0095593 25.0504252
2 28.2012995 92.6157463
2 9.4341061 95.8249016
2 2.5321764 26.2684983
d-ul potential
5
0 87.6328721 3.0000000
1 61.7373377 22.5533557
2 32.4385104 178.1241988
2 8.7537199 76.9924162
2 1.6633189 9.4818270
2.10 charge
Write "charge" to specify nuclear charges.
A dummy atom is set using X in geom section to specify a point charge.
The format of nuclear charges is as follows.
(atom number in geom section) (nuclear charge)
(atom number in geom section) (nuclear charge)
A blank line or the end of the file means the end of the
charge function section.
e.g.) geom
O 0.0 0.0 0.0
H 1.0 0.0 0.0
H 0.0 1.0 0.0
X 0.0 0.0 1.5
X 0.0 0.0 -2.0
charge
4 1.0
5 -0.5