# Fileset [toast-0.6.0-manual-0.8-en.pdf](https://mdr.nims.go.jp/filesets/c1472932-9115-4916-bdfa-7d065c3ac856/download) ## Creator [XU, Yibin](https://orcid.org/0000-0001-8600-8748), [ARAI, Masao](https://orcid.org/0000-0003-0088-5649) ## Rights MIT License ## Other metadata [TOAST: Template Oriented Atomic Simulation Toolkit](https://mdr.nims.go.jp/datasets/168ba0db-5396-4389-89f7-c976ffa101af) ## Fulltext ■ ■ First principle automatic calculation program Template Oriented Atomic Simulation Toolkit (TOAST) User's Manual toast-0.6.0-manual-0.8 2019/11/29 ■ ■ 1 Contents 1. Outline of the program ............................................................................................................................................... 3 2. Installing programs, setting preferences ................................................................................................................. 4 2.1 Operating Environment / Environment Setting ............................................................................................... 4 2.1.1 Installing Python ............................................................................................................................................ 4 2.1.2 First principle calculation program ............................................................................................................. 4 2.1.3 Visualization of calculation results .............................................................................................................. 4 2.2 Installation ............................................................................................................................................................. 5 2.3 Environment setting ............................................................................................................................................. 5 2.3.1 Editing a calculation scenario configuration file ........................................................................................ 5 2.3.2 Editing of job execution configuration file ................................................................................................... 6 3. Usage of the program .................................................................................................................................................. 7 3.1 Overview ................................................................................................................................................................. 7 3.2 Calculation parameters ........................................................................................................................................ 8 3.3 Configuration file ................................................................................................................................................. 13 3.3.1 Common configuration file (toast.cfg) ........................................................................................................ 13 3.3.2 Calculation scenario configuration file ...................................................................................................... 14 3.3.3 Pseudopotential configuration file .............................................................................................................. 15 3.3.4 Example of configuration file (default) .................................................................................................... 15 3.3.4.1 Example of configuration file (VASP).................................................................................................. 15 3.3.4.1 Example of configuration file (Quantum ESPRESSO) .................................................................... 19 3.3.4.1 Example of configuration file (ABINIT) ........................................................................................... 25 3.3.5 Job execution configuration file .................................................................................................................. 30 3.3.6 Example of job execution configuration file .............................................................................................. 30 3.3.6.1 Example of configuration file (PBS) .................................................................................................... 30 3.4 Execution of program .......................................................................................................................................... 32 3.4.1 Automatic calculation of multiple materials ............................................................................................. 32 3.4.2 Automatic calculation of multiple materials (Job status update / Add submit) .................................. 32 3.4.3 First principle automatic calculation of one crystal structure ............................................................... 33 3.4.4 Calculated data list ...................................................................................................................................... 34 3.4.5 Calculation status ......................................................................................................................................... 35 3.4.6 Visualization Data ........................................................................................................................................ 36 3.5 Calculation data ................................................................................................................................................... 38 3.5.1 Outline of calculation data .......................................................................................................................... 38 3.5.2 First principle automatic calculation data file calculations.xml ......................................................... 39 4. Details of the program .............................................................................................................................................. 44 4.1 Structure of program ........................................................................................................................................... 44 4.2 Functions of main class....................................................................................................................................... 45 4.2.1 calculation./autocalc.py ................................................................................................................................ 45 4.2.2 calculation./calc.py ........................................................................................................................................ 45 4.2.3 calculation./calculator.py.............................................................................................................................. 45 4.2.4 calculation./vasp.py ...................................................................................................................................... 46 4.2.5 calculation./espresso.py ................................................................................................................................ 46 4.2.6 calculation./abinit.py .................................................................................................................................... 46 4.2.7 structure/crystal.py ...................................................................................................................................... 47 4.2.8 jobmanage/job.py .......................................................................................................................................... 47 4.2.9 calculation/calprop.py................................................................................................................................... 47 2 4.2.10 calculation/calvis.py ................................................................................................................................... 47 3 1. Outline of the program The first principle automatic calculation program is a program that executes first principles calculation for a crystal structure (CIF file) prepared by a user. The first principle calculation program assumes that the program available to the user is used. The outline of the first principle automatic calculation program is shown in Fig. 1.1. Fig.1.1 Outline of First Principle Automatic Calculation Program Main features of the first principles calculation program are shown below.  It consists of Python programs, and it runs on command basis in the Linux environment.  he interface of the first principle automatic calculation program corresponds to the following first principle calculation program. ・ The Vienna Abinitio Simulation Package (VASP) （http://www.vasp.at/） ・ Quantum ESPRESSO （http://www.quantum-espresso.org/） ・ ABINIT （http://www.abinit.org/）  Execute first principles calculations sequentially based on the system or user prepared calculation scenario.  By editing the configuration file, it can be used according to the user environment. Calculation serverFirst principles calculation program VASP, Quantum Espresso, ABINNIT, …Material (crystal structure)(User prepared)First Principle CalculationData analysisEnergy, Charge Density, DOS, Band Structure, ...Calculation DataVisualizationCalculation scenarioexecution programCrystal structureanalysis programData analysisprogramInput data (common data)Atomic structure, calc. parameters, k pointPotential dataJob scriptCalculation data (common data)Data analysis dataInput data, execution script, output dataFirst principles calculation program interfaceCrystal structureCIF fileAtomWork, ICSDCrystal structure softwareVESTA, CrystalXXX, ...First principle automatic calculation programFirst principles calculation dataCommon format (XML file)First principles calculation programinterfaceCommon format (XML file)⇔ Input / Output file⇔ Job script (PBS type)User configuration fileCalculation scenario, calculation parametersJob script (template)programCommand useAtom / molecule Visualization softwareJmol, VESTA, XCrysDen,Graph creation softwareGnuplot, 4 2. Installing programs, setting preferences 2.1 Operating Environment / Environment Setting The first principle automatic calculation program is assumed to be used in the computer of the Linux environment. Required applications are shown below. Item Application Remarks Python execution environment Python 3.X Standard package Needs numpy First principles calculation program execution environment First principles calculation program VASP, Quantum Espresso , ABINIT Calculation result visualization environment Gnuplot Crystal structure visualization application 2.1.1 Installing Python The Python package can be installed as a distribution package for many Linux distributions. In addition to the standard package of Python package, installation of Python package numpy is necessary. Or download the Python package and do the build. (https://www.python.org) 2.1.2 First principle calculation program The first principle calculation program assumes that the program available to the user is used. The interface of the first principles calculation program corresponds to the following first principle calculation program. First principles calculation program First principles calculation program Operation confirmation version Web site The Vienna Abinitio Simulation Package (VASP) VASP 5.4.4 http://www.vasp.at/ Quantum ESPRESSO QE 6.4.1 http://www.quantum-espresso.org/ ABINIT ABINIT 8.10.3 http://www.abinit.org/ For compiling and using the first principles calculation program, please refer to the manual of each program, website. 2.1.3 Visualization of calculation results The visualization of the calculation result of the first principles calculation program can be carried out by a commercially available application or public use the application. Item Data Format Applications Crystal Structure CIF file Input / output data of first principles VESTA, Jmol, XCrysDen et al 5 calculation program Brillouin Zone Gnuplot script Jmol script Gnuplot Jmol Charge Density Gaussian Cube VESTA, Jmol, Xcrysden, 他 Density of State Gnuplot 他 Band Structure Gnuplot 他 2.2 Installation Deploy archive toast-X.X.X.tar.gz of the first principle automatic calculation program in the directory to install. Structure of the first principle automatic calculation program Install Directory Subdirectory Contents toast-X.X.X config Configuration file calc Python programs test Sample data for test 2.3 Environment setting The first principle automatic calculation program edits the setting file in toast / config according to the user's computing environment. The configuration file is in the Config File format (RFC 822 format), it is divided into sections by the header [sectioin], parameters and values are described in the form of name = value in each section. * Details of the configuration file are described in Chapter 3. Configuration file list Item File Contents Common configuration file toast.cfg Common configuration file Job management, Calculation scenario Calculation scenario configuration file vasp.para.cfg espresso..para.cfg abinit.para.cfg Configuration file for VASP Configuration file for Quantum ESPRESSO Configuration file for ABINIT Pseudopotential configuration file vasp.pp.XXX.txt espresso.pp.XXX.txt abinit.pp.XXX.txt Potential list for VASP Potential list for QE Potential list for ABINIT Job execution configuration file jobmanage.cfg jobtemplate/XXX.tmpl Configuration of Job management system 2.3.1 Editing a calculation scenario configuration file Describe the following items of the calculation scenario setting file of each calculation program according to the execution environment of the user's first principle calculation program. Calculation scenario configuration file [general] section Item Contents Description example 6 ppdir Directory of pseudopotential file ppdir = /opt/app/vasp/potpaw_PBE ppdir = /opt/app/espresso/SSSP_eff_PBE ppdir = /opt/app/abinit/JTH-PBE-atomicdata-1.0 cmd Execution command of calculation program cmd = /opt/app/vasp/vasp.5.3.5/vasp cmd = /opt/app/espresso/espresso-5.4.0/bin/pw.x cmd = /opt/app/abinit/abinit-8.0.8/bin/abinit 2.3.2 Editing of job execution configuration file When using the job management system, edit the job execution setting file and create a template of the job execution script. In the first principle automatic calculation program, a template of a PBS based job management system is prepared. Job execution configuration file [general] section Item Contents Description example jobmanage_type Specify the type of job execution interactive interactive execution section-name Use job management system jobmanage_type = interactive jobmanage_type = pbs [section-name] Specify job execution script template Specify variables in the template Specify job submission command Specify job status command [pbs] template = job_template/pbs.tmpl core = 8 np = 8 queue = L ncpus = 1 nodes = 1 ppn = 8 walltime = 24:00:00 job_name = submit = qsub stat = qstat 7 3. Usage of the program 3.1 Overview The first principle automatic calculation program is a program that executes first principles calculation for a crystal structure (CIF file) prepared by a user.  It consists of Python programs, and it runs on command basis in the Linux environment.  The interface of the first principle automatic calculation program corresponds to the following first principle calculation program. ・ The Vienna Abinitio Simulation Package (VASP) （http://www.vasp.at/） ・ Quantum ESPRESSO （http://www.quantum-espresso.org/） ・ ABINIT （http://www.abinit.org/）  Execute first principles calculations sequentially based on the system or user prepared calculation scenario.  By editing the configuration file, it can be used according to the user environment. The processing outline of the first principle automatic calculation program is as follows.  Read multiple crystal structures (CIF File) easy for the user  Create a calculation directory for each crystal structure (Material ID)  Generate input data and generate a job execution script based on the calculation scenario (calculation scenario setting file) and execute calculation。  Calculated data is extracted and output to an automatic calculation data file.  Analyze calculation results such as band gap.  Output the crystal structure, charge density, state density distribution, band structure in a data format that can be visualized by commercially available / published applications。 Fig.3.1 Outline of processing of automatic calculation program VASPFirst Principle CalculationData analysisEnergy, Charge Density, DOS, Band Structure, ...First principles calculation program interfaceFirst principle calculation programAtom / molecule visualization softwareJmol, VESTA, XCrysDen,Graph creation softwareGnuplot,ABINIT Quantum EspressoCalculation scenarioCfg filePP List FileCrystal structureCIF fileInput dataExecution scriptOutput data Calc Folder(Material)Intermediate FormatXML fileCalculation result dataCrystal structure CIFCharge DensityDOS, Band StructureCalculation result listFirst principle automatic calculation systemUser interface 8 3.2 Calculation parameters Calculation parameters such as energy cutoff, exchange correlation term, SCF calculation iteration method, structure optimization method, convergence judgment value, etc. of the first principle calculation program are described in the calculation scenario setting file. The unit cell (Primitive Cell) of calculation dependent on the crystal structure, the relative coordinates of atoms, the k point mesh, the k point route of the band structure calculation, the number of bands depending on the pseudopotential, etc. are calculated in the automatic calculation program. Item Calculation method Crystal structure Atom list (atom coordinates) Calculate Conventional Cell, Primitive Cell, atom list (atomic coordinates) from crystal_system, spacegroup, cell_length, cell_angle, symmetry, atom of CIF File K point mesh In calculation scenario setting file, length l is specified with _kpoints_length and calculated. bi, Reciprocal Lattice Vector Nkx = max(4, l * |b1|+0.5) Nky = max(4, l * |b2|+0.5) Nkz = max(4, l * |b3|+0.5) In the calculation scenario setting file, spacing s is specified with _kpoints_spacing and calculated. Nkx = max(4, |b1| / s +0.5) Nky = max(4, |b2| / s +0.5) Nkz = max(4, |b3| / s +0.5) Number of bands Extract the value of Z Valence of the pseudopotential of each element. Calculate Electron number Nelect from Z Valence and the number of atoms of each element. Nbands = int(Nelect*0.6+0.5) + max(4, Natom*2) k point path for the band calculation Find the Brillouin Zone from crystal_system, spacegroup, cell_length, cell_angle, symmetry of CIF File and calculate k point path. k point path for the band calculation 分類 System Center Type Condition K points Path, K Points Simple cubic lattice cubic simple A＝B＝C α＝β＝γ＝90 Delta G(0.0 0.0 0.0) X(0.5 0.0 0.0) Z X(0.5 0.0 0.0) M(0.5 0.5 0.0) Sigma M(0.5 0.5 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) R(0.5 0.5 0.5) T R(0.5 0.5 0.5) M(0.5 0.5 0.0) S X(0.5 0.0 0.0) R(0.5 0.5 0.5)) Face centered cubic lattice cubic face A＝B＝C α＝β＝γ＝90 Delta G(0.0 0.0 0.0) X(1.0 0.0 0.0) Z X(1.0 0.0 0.0) W(1.0 0.5 0.0) Q W(1.0 0.5 0.0) L(0.5 0.5 0.5) Lambda L(0.5 0.5 0.5) G(0.0 0.0 0.0) Sigma G(0.0 0.0 0.0) K(0.75 0.75 0.0) S U(1.0 0.5 0.5) X(1.0 0.0 0.0) Body centered cubic lattice cubic body A＝B＝C α＝β＝γ＝90 Delta G(0.0 0.0 0.0) H(1.0 0.0 0.0) G H(1.0 0.0 0.0) N(0.5 0.5 0.0) 9 Sigma N(0.5 0.5 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) P(0.5 0.5 0.5) D P(0.5 0.5 0.5) N(0.5 0.5 0.0) F H(1.0 0.0 0.0) P(0.5 0.5 0.5) Hexagonal lattice hexagonal simple A＝B≠C α＝β＝90 γ＝120 Sigma G(0.0 0.0 0.0) M(0.5 0.0 0.0) T' M(0.5 0.0 0.0) K(1.0/3 1.0/3 0.0) T K(1.0/3 1.0/3 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) A(0.0 0.0 0.5) R A(0.0 0.0 0.5) L(0.5 0.0 0.5) S' L(0.5 0.0 0.5) H(1.0/3 1.0/3 0.5) S H(1.0/3 1.0/3 0.5) A(0.0 0.0 0.5) U L(0.5 0.0 0.5) M(0.5 0.0 0.0) P K(1.0/3 1.0/3 0.0) H(1.0/3 1.0/3 0.5) Trigonal lattice 1 trigonal simple type1 A＝B＝C α＝β＝γ α＜90 Q F(0.0 0.5 1.0) n1(2eta 0.5-eta 1.0) Sigma n1(eta eta 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) Z(0.0 0.0 1.5) B Z(0.0 0.0 1.5) n2(-eta 2eta 1.5) Y n2(0.5-eta 2eta 0.5) L(0.5 0.0 0.5) l1 L(0.5 0.0 0.5) G(0.0 0.0 0.0) Trigonal lattice 2 trigonal simple type2 A＝B＝C α＝β＝γ α≧90 Sigma F(0.5 0.5 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) n1(0.0 0.0 eta) P n1(1.0 0.0 eta) Z(1.0 0.0 -0.5) Y Z(0.0 1.0 0.5) L(0.5 0.0 0.5) l1 L(0.5 0.0 0.5) G(0.0 0.0 0.0) Simple tetoragonal lattice tetragonal simple A＝B≠C α＝β＝γ＝90 Delta G(0.0 0.0 0.0) X(0.5 0.0 0.0) Y X(0.5 0.0 0.0) M(0.5 0.5 0.0) Sigma M(0.5 0.5 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) Z(0.0 0.0 0.5) U Z(0.0 0.0 0.5) R(0.5 0.0 0.5) T R(0.5 0.0 0.5) A(0.5 0.5 0.5) S A(0.5 0.5 0.5) Z(0.0 0.0 0.5) W R(0.5 0.0 0.5) X(0.5 0.0 0.0) V M(0.5 0.5 0.0) A(0.5 0.5 0.5) Body centered tetragonal lattice 1 tetragonal body type1 A＝B≠C α＝β＝γ＝90 A＝B＜C Lambda Z(0.0 0.0 1.0) G(0.0 0.0 0.0) Sigma G(0.0 0.0 0.0) n1(eta 0.0 0.0) F n1(eta 0.0 1.0) Z(0.0 0.0 1.0) U Z(0.0 0.0 1.0) n2(eta eta 1.0) Y n2(eta 1.0-eta 0.0) X(0.5 0.5 0.0) Delta X(0.5 0.5 0.0) G(0.0 0.0 0.0) W X(0.5 0.5 0.0) P(0.5 0.5 0.5) Q P(0.5 0.5 0.5) N(0.5 0.0 0.5) Body centered tetragonal tetragonal body type2 A＝B≠C α＝β＝γ＝90 V Z(1.0 0.0 0.0) n1(1.0 0.0 eta) Lambda n1(0.0 0.0 eta) G(0.0 0.0 0.0) 10 lattice 2 A＝B＞C Sigma G(0.0 0.0 0.0) Z(1.0 0.0 0.0) Y Z(1.0 0.0 0.0) X(0.5 0.5 0.0) Delta X(0.5 0.5 0.0) G(0.0 0.0 0.0) W X(0.5 0.5 0.0) P(0.5 0.5 0.5) Q P(0.5 0.5 0.5) N(0.5 0.0 0.5) Simple orthorombic lattice orthorhombic simple A≠B≠C α＝β＝γ＝90 Sigma G(0.0 0.0 0.0) X(0.5 0.0 0.0) D X(0.5 0.0 0.0) S(0.5 0.5 0.0) C S(0.5 0.5 0.0) Y(0.0 0.5 0.0) Delta Y(0.0 0.5 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) Z(0.0 0.0 0.5) A Z(0.0 0.0 0.5) U(0.5 0.0 0.5) P U(0.5 0.0 0.5) R(0.5 0.5 0.5) E R(0.5 0.5 0.5) T(0.0 0.5 0.5) B T(0.0 0.5 0.5) Z(0.0 0.0 0.5) G U(0.5 0.0 0.5) X(0.5 0.0 0.0) Q S(0.5 0.5 0.0) R(0.5 0.5 0.5) H T(0.0 0.5 0.5) Y(0.0 0.5 0.0) Face centered orthorombic lattice 1 orthorhombic face type1 A≠B≠C α＝β＝γ＝90 ka^2 < kb^2 + kc^2 kb^2 < kc^2 + ka^2 kc^2 < ka^2 + kb^2 Lambda Z(0.0 0.0 1.0 ) G(0.0 0.0 0.0) Sigma G(0.0 0.0 0.0) X(1.0 0.0 0.0) D X(1.0 0.0 0.0) n1(1.0 eta 0.0) B n1(0.0 eta 1.0) Z(0.0 0.0 1.0) A Z(0.0 0.0 1.0) n2(eta 0.0 1.0) C n2(eta 1.0 0.0) Y(0.0 1.0 0.0) Delta Y(0.0 1.0 0.0) G(0.0 0.0 0.0) H Y(0.0 1.0 0.0) n3(0.0 1.0 eta) G n3(1.0 0.0 eta) X(1.0 0.0 0.0) Face centered orthorombic lattice 2 orthorhombic face type2 A≠B≠C α＝β＝γ＝90 ka^2 > kb^2 + kc^2 Lambda Z(0.0 0.0 1.0) G(0.0 0.0 0.0) Sigma G(0.0 0.0 0.0) n1(eta 0.0 0.0) U n1(eta 1.0 1.0) X(0.0 1.0 1.0) B X(0.0 1.0 1.0) Z(0.0 0.0 1.0) A Z(0.0 0.0 1.0) n2(eta 0.0 1.0) C n2(eta 1.0 0.0) Y(0.0 1.0 0.0) Delta Y(0.0 1.0 0.0) G(0.0 0.0 0.0) H Y(0.0 1.0 0.0) X(0.0 1.0 1.0) Face centered orthorombic lattice 3 orthorhombic face type3 A≠B≠C α＝β＝γ＝90 kb^2 > kc^2 + ka^2 Lambda Z(0.0 0.0 1.0) G(0.0 0.0 0.0) Sigma G(0.0 0.0 0.0) X(1.0 0.0 0.0) D X(1.0 0.0 0.0) n2(1.0 eta 0.0) B n2(0.0 eta 1.0) Z(0.0 0.0 1.0) A Z(0.0 0.0 1.0) Y(1.0 0.0 1.0) R Y(1.0 0.0 1.0) n1(1.0 eta 1.0) Delta n1(0.0 eta 0.0) G(0.0 0.0 0.0) G Y(1.0 0.0 1.0) X(1.0 0.0 0.0) 11 Face centered orthorombic lattice 4 orthorhombic face type4 A≠B≠C α＝β＝γ＝90 kc^2 > ka^2 + kb^2 Q Z(1.0 1.0 0.0) n1(1.0 1.0 eta) Lambda n1(0.0 0.0 eta) G(0.0 0.0 0.0) Sigma G(0.0 0.0 0.0) X(1.0 0.0 0.0) D X(1.0 0.0 0.0) Z(1.0 1.0 0.0) C Z(1.0 1.0 0.0) Y(0.0 1.0 0.0) Delta Y(0.0 1.0 0.0) G(0.0 0.0 0.0) H Y(0.0 1.0 0.0) n2(0.0 1.0 eta) G n2(1.0 0.0 eta) X(1.0 0.0 0.0) Body centered orthorombic lattice 1 orthorhombic body type1 A≠B≠C α＝β＝γ＝90 A＞B A＞C Sigma G(0.0 0.0 0.0) X(1.0 0.0 0.0) U X(1.0 0.0 0.0) n1(1.0 eta 0.0) Delta n1(0.0 eta 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) n2(0.0 0.0 eta) G n2(1.0 0.0 eta) X(1.0 0.0 0.0) Q R(0.5 0.0 0.5) W(0.5 0.5 0.5) D W(0.5 0.5 0.5) S(0.0 0.5 0.5) P T(0.5 0.5 0.0) W(0.5 0.5 0.5) Body centered orthorombic lattice 2 orthorhombic body type2 A≠B≠C α＝β＝γ＝90 B＞C B＞A Sigma G(0.0 0.0 0.0) n2(eta 0.0 0.0) F n2(eta 1.0 0.0) X(0.0 1.0 0.0) Delta X(0.0 1.0 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) n1(0.0 0.0 eta) G n1(0.0 1.0 eta) X(0.0 1.0 0.0) Q R(0.5 0.0 0.5) W(0.5 0.5 0.5) D W(0.5 0.5 0.5) S(0.0 0.5 0.5) P T(0.5 0.5 0.0) W(0.5 0.5 0.5) Body centered orthorombic lattice 3 orthorhombic body type3 A≠B≠C α＝β＝γ＝90 C＞A C＞B Sigma G(0.0 0.0 0.0) n1(eta 0.0 0.0) F n1(eta 0.0 1.0) X(0.0 0.0 1.0) U X(0.0 0.0 1.0) n2(0.0 eta 1.0) Delta n2(0.0 eta 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) X(0.0 0.0 1.0) Q R(0.5 0.0 0.5) W(0.5 0.5 0.5) D W(0.5 0.5 0.5) S(0.0 0.5 0.5) P T(0.5 0.5 0.0) W(0.5 0.5 0.5) Base centered orthorombic lattice 1 orthorhombic base type1 A≠B≠C α＝β＝γ＝90 A＜B Sigma G(0.0 0.0 0.0) n1(eta 0.0 0.0) C n1(eta 1.0 0.0) Y(0.0 1.0 0.0) Delta Y(0.0 1.0 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) Z(0.0 0.0 0.5) A Z(0.0 0.0 0.5) n2(eta 0.0 0.5) E n2(eta 1.0 0.5) T(0.0 1.0 0.5) B T(0.0 0.0 0.5) Z(0.0 1.0 0.5) H Y(0.0 1.0 0.0) T(0.0 1.0 0.5) 12 D S(0.5 0.5 0.0) R(0.5 0.5 0.5) Base centered orthorombic lattice 2 orthorhombic base type2 A≠B≠C α＝β＝γ＝90 A＞B Sigma G(0.0 0.0 0.0) Y(1.0 0.0 0.0) F Y(1.0 0.0 0.0) n1(1.0 eta 0.0) Delta n1(0.0 eta 0.0) G(0.0 0.0 0.0) Lambda G(0.0 0.0 0.0) Z(0.0 0.0 0.5) A Z(0.0 0.0 0.5) T(1.0 0.0 0.5) G T(1.0 0.0 0.5) n2(1.0 eta 0.5) B n2(0.0 eta 0.5) Z(0.0 0.0 0.5) H Y(1.0 0.0 0.0) T(1.0 0.0 0.5) D S(0.5 0.5 0.0) R(0.5 0.5 0.5) Simple monoclinic lattice monoclinic simple A≠B≠C α＝γ＝90 β＞90 Lambda G(0.0 0.0 0.0) Y(0.0 0.5 0.0) l1 Y(0.0 0.5 0.0) C(0.0 0.5 0.5) W C(0.0 0.5 0.5) Z(0.0 0.0 0.5) l2 Z(0.0 0.0 0.5) G(0.0 0.0 0.0) l3 G(0.0 0.0 0.0) X(0.5 0.0 0.0) V X(0.5 0.0 0.0) A(0.5 0.5 0.0) l4 A(0.5 0.5 0.0) Y(0.0 0.5 0.0) l5 Y(0.0 0.5 0.0) E(0.5 0.5 -0.5) U E(0.5 0.5 -0.5) D(0.5 0.0 -0.5) l6 D(0.5 0.0 -0.5) G(0.0 0.0 0.0) Base monoclinic lattice 1 monoclinic base type1 A≠B≠C α＝γ＝90 β＞90 A＜B Lambda G(0.0 0.0 0.0) Y(0.0 1.0 0.0) l1 Y(0.0 1.0 0.0) n1(eta 1.0 0.0) l2 n1(eta 0.0 0.0) G(0.0 0.0 0.0) l3 G(0.0 0.0 0.0) Z(0.0 0.0 0.5) U Z(0.0 0.0 0.5) M(0.0 1.0 0.5) l4 M(0.0 1.0 0.5) Y(0.0 1.0 0.0) Base monoclinic lattice 2 monoclinic base type2 A≠B≠C α＝γ＝90 β＞90 A＞B Lambda G(0.0 0.0 0.0) n1(0.0 eta 0.0) C n1(1.0 eta 0.0) Y(1.0 0.0 0.0) l1 Y(1.0 0.0 0.0) G(0.0 0.0 0.0) l2 G(0.0 0.0 0.0) Z(0.0 0.0 0.5) U Z(0.0 0.0 0.5) n2(0.0 eta 0.5) E n2(1.0 eta -0.5) M(1.0 0.0 -0.5) l3 M(1.0 0.0 -0.5) Y(1.0 0.0 0.0) 13 3.3 Configuration file 3.3.1 Common configuration file (toast.cfg) Common setting file toast.cfg sets common settings for job management and calculation scenarios for each program. The settings in the common settings file take precedence over the calculation scenario settings file and job management settings file. Section name value [job] jobmanage_type interactive [section-name] Interactive execution Generate job script using template and variable specified in [section] mpi_cmd Specify a job script template nproc Number of MPI execution processes [vasp] program Specify the calculation program version Program version ppdir Specify the directory of the potential file pplist Specify the potential list file cmd Specify execution command of calculation program scenario Specify Calculation scenario [espresso] program Specify the calculation program version Program version ppdir Specify the directory of the potential file pplist Specify the potential list file cmd Specify execution command of calculation program scenario Specify Calculation scenario [abinit] program Specify the calculation program version Program version ppdir Specify the directory of the potential file pplist Specify the potential list file cmd Specify execution command of calculation program scenario Specify Calculation scenario 14 3.3.2 Calculation scenario configuration file The first principle automatic calculation program edits the configuration file in toast / config according to the user's computing environment. The configuration file is in the Config File format (RFC 822 format), it is divided into sections by the header [sectioin], parameters and values are described in the form of name = value in each section. Lines beginning with # are comment lines. * Using the Python ConfigParser module.  Execute multiple tasks in order according to the scenario specified by the user for the prepared CIF file.  Configuration file is divided into sections with header [section-name].  [general] section, [default] section The following sections set tasks to be executed sequentially.  Each task consists of a unique parameter (_name) and a parameter (name) of the calculation program.  The parameters of the calculation program are the keywords themselves of the input data of the first principles calculation program. Section name value [geneal] program vasp espresso abinit Specify the calculation program VASP Quantum ESPRESSO ABINIT version Program version ppdir Specify the directory of the potential file pplist Specify the potential list file cmd Specify execution command of calculation program [default] _kpoints_length 30 Specify length in K point mesh generation _kpoints_spacing 0.3 Specify spacing in K point mesh generation _spin nomag ferro Specify spin calculation nomag calculatiion ferro calculatiion name value Common calculation program parameters in each [task] section In each [task] section, if _input = default is specified, these calculation parameters are added [task] _calc_dir Specify subdirectory to execute [task] _structure cif task名 Crystal structure of CIF file Crystal structure of calculation result of [task] _input default In each [task] section, the calculation parameter of [default] is added _spin_criteion 0.1 Spin determination value in spin determination calculation Valid when Task name is [check_spin] _mkdir_X Specify subdirectory to generate _copy_X [src] [dist] Copy files _name_list_X control system electrons Namalist of input data (for QE) 15 name value Calculation program parameters 3.3.3 Pseudopotential configuration file In the calculation of the first principle calculation program, the potential of each element to be used is set. The first principle automatic calculation program prepares a pseudopotential setting file for each first principles calculation program. Program Configuration file Pseudopotential Remarks VASP potpaw_PBE.rec.txt Potpaw_PBE Recommended potential of VASP QE espresso.pp.pbe.sssp.eff.txt SSSP_eff_PBE Standard Solid State Pseudopotentials (SSSP) http://materialscloud.org/sssp/ espresso.pp.pbe.gbrv.txt GBRV pbe_UPF GBRV pseudopotential http://www.physics.rutgers.edu/gbrv/ ABINIT abinit.pp.pbe.jth.txt JTH PAW JTH PAW atomic datasets http://www.abinit.org/ Description of pseudopotential setting file [Atomic number] [element name] [potential file / directory] … 3.3.4 Example of configuration file (default) 3.3.4.1 Example of configuration file (VASP) An example configuration file for VASP is shown below. (1) Calculation scenario configuration file Spin determination calculation, structure optimization calculation, SCF calculation, DOS calculation, BAND calculation are sequentially calculated scenarios. [general] program = vasp version = 5.3.5 ppdir = /opt/app/vasp/potpaw_PBE pplist = vasp.pp.pbe.rec.txt cmd = /opt/app/vasp/vasp.5.3.5/vasp #mpi_cmd = mpijob -mpi nproc = 1 [default] _kpoints_length = 30 #_kpoints_spacing = 0.03 #_spin = nonmag #_spin = ferro NPAR = 1 SYSTEM = ISTART = 0 16 PREC = high ENCUT = 550 ALGO = fast #ALGO = normal EDIFF = 1E-6 NELM = 100 # default 60 #NELMIN = 8 #NELMDL = -5 ISPIN = NBANDS = ISMEAR = 0 # default 1 SIGMA = 0.1 # default 0.2 ISYM = [check_spin] _calc_dir = spin _structure = cif _input = default _spin_criterion = 0.1 ISPIN = 2 LWAVE = .FALSE. LCHARG = .FALSE. IBRION = 2 ISIF = 3 NSW = 100 EDIFFG = 1e-5 POTIM = 0.05 [opt1] _calc_dir = opt.1 _structure = cif _input = default NELMIN = 8 LWAVE =.FALSE. LCHARG =.FALSE. IBRION =2 ISIF = 3 NSW = 200 EDIFFG = 1e-5 POTIM = 0.05 [opt2] _calc_dir = opt.2 _structure = opt1 _input = default NELMIN = 8 LWAVE =.FALSE. LCHARG =.FALSE. IBRION =2 17 ISIF = 3 NSW = 200 EDIFFG = -0.01 POTIM = 0.05 [scf] _calc_dir = scf _structure = opt2 _input = default NELMIN = 8 ISMEAR = -5 LAECHG = .TRUE. [dos] _calc_dir = dos _structure = scf _input = default _copy_2 = ../scf/WAVECAR WAVECAR _copy_3 = ../scf/CHGCAR CHGCAR NELMIN = 8 ISMEAR = -5 ICHARG = 11 LORBIT = 11 _emin_ef = -20 _emax_ef = +20 EMIN = -20 EMAX = 30 NEDOS = 2501 LWAVE = .FALSE. [band] _calc_dir = band _structure = scf _input = default _copy_2 = ../scf/WAVECAR WAVECAR _copy_3 = ../scf/CHGCAR CHGCAR ISMEAR = SIGMA = ICHARG = 11 LWAVE = .FALSE. (2) Pseudopotential configuration file 1 H H 2 He He 3 Li Li_sv 4 Be Be 5 B B 6 C C 18 7 N N 8 O O 9 F F 10 Ne Ne 11 Na Na_pv 12 Mg Mg 13 Al Al 14 Si Si 15 P P 16 S S 17 Cl Cl 18 Ar Ar 19 K K_sv 20 Ca Ca_sv 21 Sc Sc_sv 22 Ti Ti_sv 23 V V_sv 24 Cr Cr_sv_GW 25 Mn Mn_pv 26 Fe Fe 27 Co Co 28 Ni Ni 29 Cu Cu 30 Zn Zn 31 Ga Ga_d 32 Ge Ge_d 33 As As 34 Se Se 35 Br Br 36 Kr Kr 37 Rb Rb_sv 38 Sr Sr_sv 39 Y Y_sv 40 Zr Zr_sv 41 Nb Nb_sv 42 Mo Mo_sv 43 Tc Tc_pv 44 Ru Ru_sv_GW 45 Rh Rh_sv_GW 46 Pd Pd 47 Ag Ag 48 Cd Cd 49 In In_d 50 Sn Sn_d 51 Sb Sb 52 Te Te 53 I I 54 Xe Xe 55 Cs Cs_sv 19 56 Ba Ba_sv 57 La La 58 Ce Ce 59 Pr Pr_3 60 Nd Nd_3 61 Pm Pm_3 62 Sm Sm_3 63 Eu Eu_2 64 Gd Gd_3 65 Tb Tb_3 66 Dy Dy_3 67 Ho Ho_3 68 Er Er_3 69 Tm Tm_3 70 Yb Yb_2 71 Lu Lu_3 72 Hf Hf_pv 73 Ta Ta_sv_GW 74 W W_sv 75 Re Re 76 Os Os 77 Ir Ir 78 Pt Pt 79 Au Au 80 Hg Hg 81 Tl Tl_d 82 Pb Pb_d 83 Bi Bi_d 84 Po Po_d 85 At At_d_GW 86 Rn Rn 87 Fr Fr_sv 88 Ra Ra_sv 89 Ac Ac 90 Th Th 91 Pa Pa 92 U U 93 Np Np 94 Pu Pu 95 Am Am 96 Cm Cm 3.3.4.1 Example of configuration file (Quantum ESPRESSO) An example configuration file for Quantum ESPRESSO is shown below. (1) Calculation scenario configuration file Spin determination calculation, structure optimization calculation, SCF calculation, DOS calculation, BAND 20 calculation are sequentially calculated scenarios. [general] program = espresso version = 5.4.0 #ppdir = /opt/app/espresso/upf_files ppdir = /opt/app/espresso/SSSP_eff_PBE pplist = espresso.pp.pbe.sssp.eff.txt #ppdir = /opt/app/espresso/gbrv #pplist = espresso.pp.pbe.gbrv.txt cmd = /opt/app/espresso/espresso-5.4.0/bin/pw.x nproc = 1 [default] _kpoints_length = 30 #_kpoints_spacing = 0.03 #_spin = nonmag #_spin = ferro _namelist_1 = control calculation = prefix = tstress = .true. tprnfor = .true. pseudo_dir = '../' outdir = './' wfcdir = etot_conv_thr = 1.0e-5 forc_conv_thr = 1.0e-4 disk_io = 'low' wf_collect = _namelist_2 = system ibrav = 0 nat = ntyp = nbnd = ecutwfc = 40.0 ecutrho = 200.0 occupations = 'smearing' smearing = 'gaussian' degauss = 0.1 nspin = 1 _namelist_3 = electrons mixing_beta = 0.7 conv_thr = 1.0e-6 21 _namelist_4 = ions _namelist_5 = cell [check_spin] _calc_dir = spin _structure = cif _input = default calculation = 'vc-relax' nspin = 2 [opt] _calc_dir = opt _structure = cif _input = default calculation = 'vc-relax' [scf] _calc_dir = scf _structure = opt _input = default calculation = 'scf' wfcdir = './' [charge] _calc_dir = scf _cmd = /opt/app/espresso/espresso-5.4.0/bin/pp.x _input_file = job2.in _script_file = job2.sh _log_file = log2 _namelist_1 = inputpp prefix = filplot = charge plot_num = 0 spin_component = 0 #spin_component = 1 # spin up #spin_component = 2 # spin down _namelist_2 = plot iflag = 3 output_format = 6 fileout = charge.cube [nscf] _calc_dir = dos _structure = scf _input = default _mkdir = pwscf.save _copy_1 = ../scf/pwscf.save/data-file.xml ./pwscf.save/data-file.xml _copy_2 = ../scf/pwscf.save/charge-density.dat ./pwscf.save/charge-density.dat _copy_3 = ../scf/pwscf.save/spin-polarization.dat ./pwscf.save/spin-polarization.dat 22 _copy_4 = ../scf/pwscf.paw ./pwscf.paw calculation = 'nscf' wf_collect = .true. occupations = 'tetrahedra' smearing = degauss = [tdos] _calc_dir = dos _cmd = /opt/app/espresso/espresso-5.4.0/bin/dos.x _input_file = job2.in _script_file = job2.sh _log_file = log2 _namelist = dos prefix = fildos = dos emin = emax = [pdos] _calc_dir = dos _cmd = /opt/app/espresso/espresso-5.4.0/bin/projwfc.x _input_file = job3.in _script_file = job3.sh _log_file = log3 _namelist = projwfc prefix = filpdos = pdos emin = emax = [dos_band] _calc_dir = dos _cmd = /opt/app/espresso/espresso-5.4.0/bin/bands.x _input_file = job4.in _script_file = job4.sh _log_file = log4 _namelist = bands prefix = filband = band #lsym = .true. [dos_band2] _calc_dir = dos _cmd = /opt/app/espresso/espresso-5.4.0/bin/bands.x _input_file = job5.in _script_file = job5.sh _log_file = log5 _namelist = bands 23 prefix = filband = band2 #lsym = .true. spin_component = 2 [band] _calc_dir = band _structure = scf _input = default _mkdir = pwscf.save _copy_1 = ../scf/pwscf.save/data-file.xml ./pwscf.save/data-file.xml _copy_2 = ../scf/pwscf.save/charge-density.dat ./pwscf.save/charge-density.dat _copy_3 = ../scf/pwscf.save/spin-polarization.dat ./pwscf.save/spin-polarization.dat _copy_4 = ../scf/pwscf.paw ./pwscf.paw calculation = 'bands' prefix = occupations = 'smearing' smearing = 'gaussian' degauss = 0.01 #K_POINTS = {crystal_b} [band_plot] _calc_dir = band _cmd = /opt/app/espresso/espresso-5.4.0/bin/bands.x _input_file = job2.in _script_file = job2.sh _log_file = log2 _namelist = bands prefix = filband = band #lsym = .true. [band_plot2] _calc_dir = band _cmd = /opt/app/espresso/espresso-5.4.0/bin/bands.x _input_file = job3.in _script_file = job3.sh _log_file = log3 _namelist = bands prefix = filband = band2 #lsym = .true. spin_component = 2 (2) Pseudopotential configuration file 1 H H.pbe-rrkjus_psl.0.1.UPF 2 He He_ONCV_PBE-1.0.upf 3 Li li_pbe_v1.4.uspp.F.UPF 24 4 Be Be_ONCV_PBE-1.0.upf 4 Be be_pbe_v1.4.uspp.F.UPF 5 B B.pbe-n-kjpaw_psl.0.1.UPF 6 C C_pbe_v1.2.uspp.F.UPF 7 N N.pbe.theos.UPF 8 O O_pbe_v1.2.uspp.F.UPF 9 F f_pbe_v1.4.uspp.F.UPF 10 Ne Ne.pbe-n-kjpaw_psl.1.0.0.UPF 11 Na Na_pbe_v1.uspp.F.UPF 12 Mg mg_pbe_v1.4.uspp.F.UPF 13 Al Al.pbe-n-kjpaw_psl.1.0.0.UPF 14 Si Si.pbe-n-rrkjus_psl.1.0.0.UPF 15 P P.pbe-n-rrkjus_psl.1.0.0.UPF 16 S S_pbe_v1.2.uspp.F.UPF 17 Cl cl_pbe_v1.4.uspp.F.UPF 18 Ar Ar.pbe-n-rrkjus_psl.1.0.0.UPF 19 K K.pbe-spn-rrkjus_psl.1.0.0.UPF 20 Ca Ca_pbe_v1.uspp.F.UPF 21 Sc Sc_pbe_v1.uspp.F.UPF 22 Ti ti_pbe_v1.4.uspp.F.UPF 23 V V_pbe_v1.uspp.F.UPF 24 Cr cr_pbe_v1.5.uspp.F.UPF 25 Mn Mn.pbe-spn-kjpaw_psl.0.3.1.UPF 26 Fe Fe.pbe-spn-kjpaw_psl.0.2.1.UPF 27 Co Co_pbe_v1.2.uspp.F.UPF 28 Ni ni_pbe_v1.4.uspp.F.UPF 29 Cu Cu_pbe_v1.2.uspp.F.UPF 30 Zn Zn_pbe_v1.uspp.F.UPF 31 Ga Ga.pbe-dn-rrkjus_psl.0.2.UPF 32 Ge Ge.pbe-dn-kjpaw_psl.1.0.0.UPF 33 As As.pbe-n-rrkjus_psl.0.2.UPF 34 Se Se_pbe_v1.uspp.F.UPF 35 Br br_pbe_v1.4.uspp.F.UPF 36 Kr Kr.pbe-n-rrkjus_psl.0.2.3.UPF 37 Rb Rb_ONCV_PBE-1.0.upf 38 Sr Sr.pbe-spn-rrkjus_psl.1.0.0.UPF 39 Y Y_pbe_v1.uspp.F.UPF 40 Zr Zr_pbe_v1.uspp.F.UPF 41 Nb Nb.pbe-spn-kjpaw_psl.0.3.0.UPF 42 Mo Mo_ONCV_PBE-1.0.upf 43 Tc Tc_ONCV_PBE-1.0.upf 44 Ru Ru_ONCV_PBE-1.0.upf 45 Rh Rh.pbe-spn-kjpaw_psl.1.0.0.UPF 46 Pd Pd.pbe-spn-kjpaw_psl.1.0.0.UPF 47 Ag ag_pbe_v1.4.uspp.F.UPF 48 Cd Cd.pbe-dn-rrkjus_psl.0.3.1.UPF 49 In In.pbe-dn-rrkjus_psl.0.2.2.UPF 50 Sn Sn_pbe_v1.uspp.F.UPF 51 Sb sb_pbe_v1.4.uspp.F.UPF 25 52 Te Te_pbe_v1.uspp.F.UPF 53 I I_pbe_v1.uspp.F.UPF 54 Xe Xe.pbe-dn-rrkjus_psl.1.0.0.UPF 55 Cs Cs_pbe_v1.uspp.F.UPF 56 Ba Ba_ONCV_PBE-1.0.upf 57 La La.GGA-PBE-paw-v1.0.UPF 58 Ce Ce.GGA-PBE-paw-v1.0.UPF 59 Pr Pr.GGA-PBE-paw-v1.0.UPF 60 Nd Nd.GGA-PBE-paw-v1.0.UPF 61 Pm Pm.GGA-PBE-paw-v1.0.UPF 62 Sm Sm.GGA-PBE-paw-v1.0.UPF 63 Eu Eu.GGA-PBE-paw-v1.0.UPF 64 Gd Gd.GGA-PBE-paw-v1.0.UPF 65 Tb Tb.GGA-PBE-paw-v1.0.UPF 66 Dy Dy.GGA-PBE-paw-v1.0.UPF 67 Ho Ho.GGA-PBE-paw-v1.0.UPF 68 Er Er.GGA-PBE-paw-v1.0.UPF 69 Tm Tm.GGA-PBE-paw-v1.0.UPF 70 Yb Yb.GGA-PBE-paw-v1.0.UPF 71 Lu Lu.GGA-PBE-paw-v1.0.UPF 72 Hf Hf.pbe-spn-rrkjus_psl.0.2.UPF 73 Ta Ta_pbe_v1.uspp.F.UPF 74 W W_pbe_v1.2.uspp.F.UPF 75 Re Re_pbe_v1.2.uspp.F.UPF 76 Os Os_pbe_v1.2.uspp.F.UPF 77 Ir Ir_pbe_v1.2.uspp.F.UPF 78 Pt pt_pbe_v1.4.uspp.F.UPF 79 Au Au_ONCV_PBE-1.0.upf 80 Hg Hg_pbe_v1.uspp.F.UPF 81 Tl Tl.pbe-dn-rrkjus_psl.0.2.3.UPF 82 Pb Pb.pbe-dn-kjpaw_psl.0.2.2.UPF 83 Bi Bi.pbe-dn-kjpaw_psl.0.2.2.UPF 84 Po Po.pbe-dn-rrkjus_psl.1.0.0.UPF 86 Rn Rn.pbe-dn-rrkjus_psl.1.0.0.UPF 3.3.4.1 Example of configuration file (ABINIT) An example configuration file for ABINIT is shown below. (1) Calculation scenario configuration file Spin determination calculation, structure optimization calculation, SCF calculation, DOS calculation, BAND calculation are sequentially calculated scenarios. [general] program = abinit version = 8.0.7 ppdir = /opt/app/abinit/JTH-PBE-atomicdata-1.0 pplist = abinit.pp.pbe.jth.txt 26 #ppdir = /opt/app/abinit/gbrv #pplist = abinit.pp.pbe.gbrv.txt cmd = /opt/app/abinit/abinit-8.0.8/bin/abinit #cmd = /opt/app/abinit/abinit-7.10.5/bin/abinit nproc = 1 [default] _kpoints_length = 30 #_kpoints_spacing = 0.03 #_spin = nonmag #_spin = ferro acell = rprim = ntypat = 0 znucl = natom = 0 typat = xred = nband = ecut = 30 pawecutdg = 40 iscf = 17 #ixc = 11 nstep = 100 occopt = 7 nsppol = enunit = 1 prtxml = 1 kptopt = 1 ngkpt = nshiftk = shiftk = prtcif = 1 autoparal = 1 [check_spin] _calc_dir = spin _structure = cif _input = default #_spin_criterion = 0.1 _spin_criterion = 0.0001 nsppol = 2 toldfe = 1.0e-6 #tolmxf = 0.5e-4 optcell = 1 ionmov = 2 dilatmx = 1.05 ecutsm = 0.5 ntime = 50 27 [opt1] _calc_dir = opt.1 _structure = cif _input = default toldfe = 1.0e-6 #tolmxf = 1.0e-4 optcell = 1 ionmov = 2 dilatmx = 1.05 ecutsm = 0.5 ntime = 50 [opt2] _calc_dir = opt.2 _structure = opt1 _input = default toldfe = 1.0e-6 #toldff = 1.0e-4 #tolmxf = 1.0e-4 optcell = 1 ionmov = 2 #dilatmx = 1.05 dilatmx = 1.1 ecutsm = 0.5 ntime = 50 [scf] _calc_dir = scf _structure = opt2 _input = default toldfe = 1.0e-6 [dos] _calc_dir = dos _structure = scf _input = default _copy = ../scf/jobxo_DEN jobxi_DEN iscf = -2 tolwfr = 1.0e-10 prtdos = 2 #prtdos = 3 [pdos] _calc_dir = pdos _structure = scf _input = default _copy = ../scf/jobxo_DEN jobxi_DEN iscf = -2 28 tolwfr = 1.0e-10 #prtdos = 2 prtdos = 3 [band] _calc_dir = band _structure = scf _input = default _copy = ../scf/jobxo_DEN jobxi_DEN iscf = -2 tolwfr = 1.0e-10 kptopt = 0 (2) Pseudopotential configuration file 1 H H.GGA_PBE-JTH.xml 2 He He.GGA_PBE-JTH.xml 3 Li Li.GGA_PBE-JTH.xml 4 Be Be.GGA_PBE-JTH.xml 5 B B.GGA_PBE-JTH.xml 6 C C.GGA_PBE-JTH.xml 7 N N.GGA_PBE-JTH.xml 8 O O.GGA_PBE-JTH.xml 9 F F.GGA_PBE-JTH.xml 10 Ne Ne.GGA_PBE-JTH.xml 11 Na Na.GGA_PBE-JTH.xml 12 Mg Mg.GGA_PBE-JTH.xml 13 Al Al.GGA_PBE-JTH.xml 14 Si Si.GGA_PBE-JTH.xml 15 P P.GGA_PBE-JTH.xml 16 S S.GGA_PBE-JTH.xml 17 Cl Cl.GGA_PBE-JTH.xml 18 Ar Ar.GGA_PBE-JTH.xml 19 K K.GGA_PBE-JTH.xml 20 Ca Ca.GGA_PBE-JTH.xml 21 Sc Sc.GGA_PBE-JTH.xml 22 Ti Ti.GGA_PBE-JTH.xml 23 V V.GGA_PBE-JTH.xml 24 Cr Cr.GGA_PBE-JTH.xml 25 Mn Mn.GGA_PBE-JTH.xml 26 Fe Fe.GGA_PBE-JTH.xml 27 Co Co.GGA_PBE-JTH.xml 28 Ni Ni.GGA_PBE-JTH.xml 29 Cu Cu.GGA_PBE-JTH.xml 30 Zn Zn.GGA_PBE-JTH.xml 31 Ga Ga.GGA_PBE-JTH.xml 32 Ge Ge.GGA_PBE-JTH.xml #33 As As.GGA_PBE-JTH_sp.xml 33 As As.GGA_PBE-JTH.xml 29 34 Se Se.GGA_PBE-JTH.xml 35 Br Br.GGA_PBE-JTH.xml 36 Kr Kr.GGA_PBE-JTH.xml 37 Rb Rb.GGA_PBE-JTH.xml 38 Sr Sr.GGA_PBE-JTH.xml 39 Y Y.GGA_PBE-JTH.xml 40 Zr Zr.GGA_PBE-JTH.xml 41 Nb Nb.GGA_PBE-JTH.xml 42 Mo Mo.GGA_PBE-JTH.xml 43 Tc Tc.GGA_PBE-JTH.xml 44 Ru Ru.GGA_PBE-JTH.xml 45 Rh Rh.GGA_PBE-JTH.xml 46 Pd Pd.GGA_PBE-JTH.xml 47 Ag Ag.GGA_PBE-JTH.xml 48 Cd Cd.GGA_PBE-JTH.xml #49 In In.GGA_PBE-JTH_sp.xml 49 In In.GGA_PBE-JTH.xml #50 Sn Sn.GGA_PBE-JTH_sp.xml 50 Sn Sn.GGA_PBE-JTH.xml #51 Sb Sb.GGA_PBE-JTH_sp.xml 51 Sb Sb.GGA_PBE-JTH.xml 52 Te Te.GGA_PBE-JTH.xml 53 I I.GGA_PBE-JTH.xml 54 Xe Xe.GGA_PBE-JTH.xml 55 Cs Cs.GGA_PBE-JTH.xml 56 Ba Ba.GGA_PBE-JTH.xml 57 La La.GGA_PBE-JTH.xml 58 Ce Ce.GGA_PBE-JTH.xml 59 Pr Pr.GGA_PBE-JTH.xml 60 Nd Nd.GGA_PBE-JTH.xml 61 Pm Pm.GGA_PBE-JTH.xml 62 Sm Sm.GGA_PBE-JTH.xml 63 Eu Eu.GGA_PBE-JTH.xml 64 Gd Gd.GGA_PBE-JTH.xml 65 Tb Tb.GGA_PBE-JTH.xml 66 Dy Dy.GGA_PBE-JTH.xml 67 Ho Ho.GGA_PBE-JTH.xml 68 Er Er.GGA_PBE-JTH.xml 69 Tm Tm.GGA_PBE-JTH.xml 70 Yb Yb.GGA_PBE-JTH.xml 71 Lu Lu.GGA_PBE-JTH.xml 72 Hf Hf.GGA_PBE-JTH.xml 73 Ta Ta.GGA_PBE-JTH.xml 74 W W.GGA_PBE-JTH.xml 75 Re Re.GGA_PBE-JTH.xml 76 Os Os.GGA_PBE-JTH.xml 77 Ir Ir.GGA_PBE-JTH.xml 78 Pt Pt.GGA_PBE-JTH.xml 79 Au Au.GGA_PBE-JTH.xml 30 80 Hg Hg.GGA_PBE-JTH.xml #81 Tl Tl.GGA_PBE-JTH_sp.xml 81 Tl Tl.GGA_PBE-JTH.xml #82 Pb Pb.GGA_PBE-JTH_sp.xml 82 Pb Pb.GGA_PBE-JTH.xml #83 Bi Bi.GGA_PBE-JTH_sp.xml 83 Bi Bi.GGA_PBE-JTH.xml 84 Po Po.GGA_PBE-JTH.xml 85 At At.GGA_PBE-JTH.xml 86 Rn Rn.GGA_PBE-JTH.xml 3.3.5 Job execution configuration file Job execution setting file jobmanage.cfg sets the format of job submission command and job script according to the user's job execution environment (job management system). For the job script format, use the template in the config / job_template directory. Section name value [general] jobmanage_type interactive [section-name] Interactive execution Generate job script using template and variable specified in [section] [type] template Specify a job script template np Number of MPI execution processes name value Specify variables in job script template 3.3.6 Example of job execution configuration file 3.3.6.1 Example of configuration file (PBS) An example job execution setting file using Torque as the PBS job management system is shown below. (1) Job execution configuration file jobmanage.cfg [general] #jobmanage_type = interactive jobmanage_type = pbs [interactive] submit = sh stat = ps [pbs] template = job_template/pbs.tmpl core = 8 np = 8 queue = L ncpus = 1 nodes = 1 31 ppn = 8 walltime = 24:00:00 job_name = submit = qsub stat = qstat (2) Job script template pbs.tmpl #!/bin/csh #PBS -q $queue #PBS -l ncpus=$ncpus #PBS -l nodes=$nodes:ppn=$ppn #PBS -l walltime=$walltime #PBS -N $job_name cd $$PBS_O_WORKDIR 32 3.4 Execution of program 3.4.1 Automatic calculation of multiple materials Read the crystal structure (CIF File) of multiple materials easier for the user, and execute sequential calculation based on the calculation scenario.  Crystal structure files are prepared by users in one directory.  Calculation data is calculated in a subdirectory for each crystal structure in the specified directory.  Material ID is set from the CIF filename. (CIF File minus the extension. Cif) Python Script Option calc/ac-setup.py -m, --matdir Directory with crystal structure (CIF File) -c, --caldir Directory where calculation is performed -p, --program Specify first principles calculation program vasp (default) espresso abinit -s, --scenario Specify calculation scenario configuration file Default System provides User scenario -n, --nproc Number of MPI execution processes Example of execution %python [INSTALLDIR]/toast/calc/ac-setup.py -m matdir -c caldir -p vasp -s vasp.para.opt.checkspin.cfg -n 8 3.4.2 Automatic calculation of multiple materials (Job status update / Add submit) Read the crystal structure (CIF File) of multiple materials easier for the user, and execute sequential calculation based on the calculation scenario.  Job status update / Add submit)  Submit new job Python Script Option calc/ac-update.py joblist joblist file joblist.txt -c, --caldir Directory where calculation is performed -n, --dry-run Status Update only No new Job submit -q, --qstat Check job management system status and update job status -v, --verbose Example of execution %python [INSTALLDIR]/toast/calc/ac-update.py –c caldir -v joblist.txt 33 3.4.3 First principle automatic calculation of one crystal structure Execute the calculation based on the calculation scenario in the directory with the crystal structure (CIF File). It is a Python script called from Python script ac-setup.py, ac-update.py which performs first principles calculation of multiple crystal structures (CIF File). Python Script Option calc/ac-calc.py -m, --mat Material ID Crystal structure (CIF File) excluding extension. Cif For AtomWork CIF files, excluding -1-2.cif -p, --program Specify first principles calculation program vasp (default) espresso abinit -s, --scenario Specify calculation scenario configuration file Default System provides User scenario -n, --nproc Number of MPI execution processes Example of execution %python [INSTALLDIR]/toast/calc/ac-calc.py -m 4295272247 -p vasp -s vasp.para.opt.checkspin.cfg -n 8 34 3.4.4 Calculated data list For a plurality of crystal structures (CIF File) easy for the user, part of calculation result of first principle automatic calculation is outputted to a text file in list format. Python Script Option calc/ac-summary.py -c, --cal Directory where calculation was performed -o, --output Output file caldata.txt Example of execution %python [INSTALLDIR]/toast/calc/ac-summary.py -c caldir Contents of Output Item Contents Remarks Material ID Information on CIF File Chemical Formula Information on CIF File Spacegroup Information on CIF File Spacegroup No Information on CIF File Lattice Parameter (original) Cell Length a, b, c Cell Angle alpha, beta, gamma Information on CIF File Lattice Parameter (relaxed) Cell Length a, b, c Cell Angle alpha, beta, gamma Total Energy (eV) Fermi Energy (eV) Bandgap Type metal, direct, indirect Bandgap (eV) Output example material chemica_formula spacegroup_name spacegroup_no lattice_parameter(original) lattice_parameter(relaxed) total_energy(eV/atom) fermi_energy(eV) bandgaptype bandgap(eV) 4295272247 Si cubic Fd-3m 227 5.429 5.429 5.429 90.0 90.0 90.0 5.4688472 5.4688472 5.4688472 90.0 90.0 90.0 -5.42460796 5.65437076 indirect 0.618 4295278799 Fe cubic Im-3m 229 2.862 2.862 2.862 90.0 90.0 90.0 2.83553114 2.83553114 2.83553114 90.0 90.0 90.0 -8.23692267 5.75646479 metal - 4295349454 O Si cubic F-43m 216 5.45 5.45 5.45 90.0 90.0 90.0 4.87188342 4.87188342 4.87188342 90.0 90.0 90.0 -5.506395975 6.30502700 metal - 35 3.4.5 Calculation status For the plurality of crystal structures (CIF File) easy for the user, the calculation status of the first principle automatic calculation is outputted to the text file in the list format. Python Script Option calc/ac-stat.py -c, --caldir Directory where calculation was performed -o, --output Output file Default calstat.txt Example of execution %python [INSTALLDIR]/toast/calc/ac-stat.py -c caldir Contents of Output 項目 内容 備考 Material ID Information on CIF File Chemical Formula Information on CIF File Spacegroup Information on CIF File Spacegroup No Information on CIF File CIF File Information on CIF File Calculation Status Calculation status o End calculation E Abnormal termination / (Calculating) - Unexecuted Calculation status of each task in calculation scenario Determination of calculation status 計算状況 VASP Quantum ESPRESSO ABINIT o End calculation vasprun.xml is normal output OUTCAR is normal output JOB DONE. Outputs to the log file (standard output) Calculation Completed is output to job.out E Abnormal termination / (Calculating) vasprun.xml is abnormal OUTCAR is abnormal JOB DONE. Is not output to log file (standard output) Calculation Completed is not output to job.out - Unexecuted vasprun.xml, OUTCAR does not exist Log file (standard output) does not exist Job.out does not exist Output example material chemica_formula spacegroup_name spacegroup_no calculation_status 4295272247 Si cubic Fd-3m 227 4295272247-1-2.cif o o o o o o 4295278799 Fe cubic Im-3m 229 4295278799-1-2.cif o o o o o o 4295349454 O Si cubic F-43m 216 4295349454-1-2.cif o o o o o o 36 3.4.6 Visualization Data The visualization data of the calculation result of the first principle calculation is output to the HTML file of the list display and the detailed display. To visualize the crystal structure, it is necessary to change the browser settings. Reference: http://wiki.jmol.org/index.php/Troubleshooting/Local_Files Python Script Option calc/ac-vis.py -c, --caldir Directory where calculation was performed -o, --output Output file default caldata.html -j, --jsdir Java Script Library Path cdn / None (default) Local User define -a, --archive Visualization data (zip file) Example of execution %python [INSTALLDIR]/toast/calc/ac-vis.py -c [caldir] -a caldata.zip Contents of Output (List) 項目 内容 備考 Material ID Information about CIF File Chemical Formula Information about CIF File Spacegroup Information about CIF File Spacegroup No Information about CIF File Lattice Parameter (original) Cell Length a, b, c Cell Angle alpha, beta, gamma Information about CIF File Lattice Parameter (relaxed) Cell Length a, b, c Cell Angle alpha, beta, gamma Total Energy (eV) Fermi Energy (eV) Bandgap Type metal, direct, indirect Bandgap (eV) Contents of Output (Detail) 項目 内容 備考 Material Information Crystal Structure Crystal System Space Group Space Group Number Cell Parameter Atom Sites Structure Conventional Cell (Initial) Primitive Cell (Initial) Primitive Cell (Relaxed) Brillouin Zone Energy Total Energy 37 Fermi Energy Band Structure Density of State Electronic Property Band Gap Band Gap Type Example of Output (List) Example of Output (Detail) 38 3.5 Calculation data 3.5.1 Outline of calculation data A sub-directory of each task (task) of the calculation scenario is created in the calculation execution directory for each crystal, and the first principle calculation is executed. The input / output data for calculation of each task (task) is stored in the subdirectory. The main calculation data are summarized in the first principle automatic calculation data file calculations.xml. In addition, a part of the calculation data is output in a data structure that can be visualized by Gnuplot visualization application or crystal structure. 項目 データファイル 内容 備考 Crystal structure [maid].cif [maid].relaxed.cif [maid].relaxed.p1cif User prepared CIF File CIF File after structure optimization CIF File after structure optimization (P1) Update lattice constant of original CIF File CIF File of P1 structure Automatic calculation data calculations.xml First principle automatic calculation data file calculations.txt Output part of calculation data Brillouin Zone [matid].bz.plt [matid].bz.spt Brillouin Zone + K point Path Gnuplot script Jmol script Charge Density [matid].charge.cube Gaussian Cube Format Visualized with VESTA, Jmol, XCrysDen etc. DOS dos.plt dos.dat Gnuplot script Simple display for check band.plt band.dat Gnuplot script Simple display for check 39 3.5.2 First principle automatic calculation data file calculations.xml The main calculation data are summarized in the first principle automatic calculation data file calculations.xml. The structure (hierarchical structure, tags, attributes) of the data file calculations.xml is shown below. データファイル calculations.xml の構成 Tag 1 Tag 2 Tag 3 Tag 4 Tag 5 Tag 6 Tag 7 calculations materials material_id chemical_formulla crystal_system spacegroup spacegroup_no cif structuire [@name=initial) Initial structure lattice [@name=conventional] a, b, c alpha,beta,gamma a1,a2,a3 Cell length Cell Angle Lat vector lattice [@name=primitive] a, b, c alpha,beta,gamma a1,a2,a3 atom i[@name=name] coordinate structuire [@name=relaxed) Optimization structure (Structure of SCF calculation) calculation [@name=task] Task calculation data inputs i[@name=value] kpoint[@type=kmesh] nkx nky nkz kpoint[@type=kpath] i[@name=KP] kx ky kz property i[@name=prop.@unit] dos spin i DOS ene dos pdos atom spin i PDOS ene pdos band spin kpoint i Band Struc ene occ Example of the data file calculations.xml 4295272247 Si cubic Fd-3m 227 4295272247-1-2.cif 40 5.429 5.429 5.429 90.0 90.0 90.0 5.429 0.0 0.0 0.0 5.429 0.0 0.0 0.0 5.429 0.0 2.7145 2.7145 2.7145 0.0 2.7145 2.7145 2.7145 0.0 0.12500 0.12500 0.12500 0.87500 0.87500 0.87500 5.4688472 5.4688472 5.4688472 90.0 90.0 90.0 5.4688472 0.0 0.0 0.0 5.4688472 0.0 0.0 0.0 5.4688472 0.0 2.7344236 2.7344236 2.7344236 0.0 2.7344236 2.7344236 2.7344236 0.0 0.12500000 0.12500000 0.12500000 0.87500000 0.87500000 0.87500000 41 … … … scf opt2 default 1 0 high 550 fast 1E-6 100 # default 60 -5 0.1 # default 0.2 8 .TRUE. 0.00000000 2.73442360 2.73442360 2.73442360 0.00000000 2.73442360 2.73442360 2.73442360 0.00000000 0.12500000 0.12500000 0.12500000 0.87500000 0.87500000 0.87500000 0.00000000 2.73442360 2.73442360 2.73442360 0.00000000 2.73442360 2.73442360 2.73442360 0.00000000 0.12500000 0.12500000 0.12500000 0.87500000 0.87500000 0.87500000 10 10 10 42 1 10 8.00000000 47 -10.84921592 -5.42460796 5.65437076 … -10.84994683 -5.424973415 5.62480381 -14.0000 0.0000 0.0000 -13.9844 0.0000 0.0000 -13.9688 0.0000 0.0000 -13.9532 0.0000 0.0000 … energy s py pz px dxy dyz dz2 dxz dx2 -14.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 -13.9844 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 -13.9688 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 -13.9532 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 -13.9376 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 … indirect 0.618 -6.1986 1.0000 5.6156 1.0000 5.6156 1.0000 … 43 … 0.00000 0.00000 0.00000 0.00000 0.02174 0.02174 0.00000 0.04348 0.04348 0.00000 0.06522 0.06522 0.00000 0.08696 0.08696 … -7.97993391 -3.989966955 5.74667513 -6.1986 1.0000 5.6156 0.9434 5.6156 0.9433 5.6156 0.9433 8.1724 -0.0000 8.1724 -0.0000 8.1724 -0.0000 8.7488 -0.0000 13.3247 0.0000 13.4902 0.0000 … 44 4. Details of the program 4.1 Structure of program The first principle automatic calculation program is composed of Python program group. The outline of the first principle automatic calculation program structure is shown below. Install Directory Subdirectory Pyhthon Program toast/calc ac-setup.py First principle automatic calculation of multiple crystal structures ac-update.py First principle automatic calculation of multiple crystal structures (Job status update / Add submit) ac-calc.py First principles calculation based on calculation scenario ac-summary.py Calculation data list output ac-stat.py Calculation status output calculation autocalc.py Class of First principle automatic calculation for multiple crystal structures calc.py Class of First principle calculation based on calculation scenario calculator.py Abstract class of processing of first principles calculation program vasp.py Class for VASP esprsso.py Class for QE abinit.py Class for ABINIT structure crystal.py Class of crystal structure analysis jobmanage job.py Class of job execution toast/config Configuration file job_template job script template 45 4.2 Functions of main class 4.2.1 calculation./autocalc.py Class of first principle automatic calculation for multiple crystal structures Class Function autocalc calculate First principle automatic calculation of multiple crystal structures calc_prep Pre-processing for automatic calculation calc Execution of automatic calculation caldata Output of calculation data list calstat Output of calculation status 4.2.2 calculation./calc.py Class of first principles calculation based on calculation scenario Class Function calc calculate First principles calculation based on calculation scenario read_config Read calculation scenario configuration file structure Generation of unit cell calc_prep Preprocessing write_parameter Generation of first principle automatic calculation data file calculations.xml calc_task Execution of each task calc_post Post-processing, calculation result analysis Update of automatic calculation data file calculations.xml kpoints Calculation of K point mesh ispin Spin decision execute Execution of first principles calculation program calstat Output of calculation status 4.2.3 calculation./calculator.py Abstract class of processing of first principles calculation program Class Function calculator calc First principles calculation based on calculation scenario potentials Generate and copy a pseudo potential file inputs Generate input data nbands Calculate number of bands structure Generation of crystal structure, atomic coordinates from calculation result of CIF File or other Task mag Extraction of magnetization for spin determination efermi Extraction of Fermi Energy for Emin, Emax in DOS calculation results Extraction of calculation result data Update of automatic calculation data file calculations.xml calstat Output of calculation status 46 4.2.4 calculation./vasp.py Class for VASP Class Function calculator calc First principles calculation based on calculation scenario potentials Generate and copy a pseudo potential file inputs Generate input data nbands Calculate number of bands structure Generation of crystal structure, atomic coordinates from calculation result of CIF File or other Task mag Extraction of magnetization for spin determination efermi Extraction of Fermi Energy for Emin, Emax in DOS calculation results Extraction of calculation result data Update of automatic calculation data file calculations.xml calstat Output of calculation status 4.2.5 calculation./espresso.py Class for Quantum ESPRESSO Class Function calculator calc First principles calculation based on calculation scenario potentials Generate and copy a pseudo potential file inputs Generate input data nbands Calculate number of bands structure Generation of crystal structure, atomic coordinates from calculation result of CIF File or other Task mag Extraction of magnetization for spin determination efermi Extraction of Fermi Energy for Emin, Emax in DOS calculation results Extraction of calculation result data Update of automatic calculation data file calculations.xml calstat Output of calculation status 4.2.6 calculation./abinit.py Class for ABINIT Class Function calculator calc First principles calculation based on calculation scenario potentials Generate and copy a pseudo potential file inputs Generate input data nbands Calculate number of bands structure Generation of crystal structure, atomic coordinates from calculation result of CIF File or other Task mag Extraction of magnetization for spin determination efermi Extraction of Fermi Energy for Emin, Emax in DOS calculation 47 results Extraction of calculation result data Update of automatic calculation data file calculations.xml calstat Output of calculation status 4.2.7 structure/crystal.py Class of crystal structure analysis Class Function calculator loadCIF Read CIF File checkCIF Check CIF File convertCIF2VASP Cell (Conventional Cell, Primitive Cell), calculation of the internal coordinates of atoms saveKPoints Calculation of k point path for band calculation saveBrillouin Output Brillouin Zone visualization script printLog Log output 4.2.8 jobmanage/job.py Class of job execution Class Function job read_config Read job execution configuration file jobscript Generate job execution script jobscript_interactive Generate execution script for Interactive calculation jobscript_template Generation of job script using template of job script of job management system 4.2.9 calculation/calprop.py 計算結果解析 Class Function cellparameter Calculate Cell parameter bandgap Calculate Bandgap fermisurf Generation of Fermi surface visualization data dosplot Generation of DOS plot data pdosplot Generation of PDOS plot data bandplot Generation of band structure plot data caldata Output Calculation data 4.2.10 calculation/calvis.py 可視化データ Class Function visdata Generate visualization data 1. Outline of the program 2. Installing programs, setting preferences 2.1 Operating Environment / Environment Setting 2.1.1 Installing Python 2.1.2 First principle calculation program 2.1.3 Visualization of calculation results 2.2 Installation 2.3 Environment setting 2.3.1 Editing a calculation scenario configuration file 2.3.2 Editing of job execution configuration file 3. Usage of the program 3.1 Overview 3.2 Calculation parameters 3.3 Configuration file 3.3.1 Common configuration file (toast.cfg) 3.3.2 Calculation scenario configuration file 3.3.3 Pseudopotential configuration file 3.3.4 Example of configuration file (default) 3.3.4.1 Example of configuration file (VASP) 3.3.4.1 Example of configuration file (Quantum ESPRESSO) 3.3.4.1 Example of configuration file (ABINIT) 3.3.5 Job execution configuration file 3.3.6 Example of job execution configuration file 3.3.6.1 Example of configuration file (PBS) 3.4 Execution of program 3.4.1 Automatic calculation of multiple materials 3.4.2 Automatic calculation of multiple materials (Job status update / Add submit) 3.4.3 First principle automatic calculation of one crystal structure 3.4.4 Calculated data list 3.4.5 Calculation status 3.4.6 Visualization Data 3.5 Calculation data 3.5.1 Outline of calculation data 3.5.2 First principle automatic calculation data file calculations.xml 4. Details of the program 4.1 Structure of program 4.2 Functions of main class 4.2.1 calculation./autocalc.py 4.2.2 calculation./calc.py 4.2.3 calculation./calculator.py 4.2.4 calculation./vasp.py 4.2.5 calculation./espresso.py 4.2.6 calculation./abinit.py 4.2.7 structure/crystal.py 4.2.8 jobmanage/job.py 4.2.9 calculation/calprop.py 4.2.10 calculation/calvis.py