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Merge pull request #14504 from mvdbeek/patrick/15-castep-datatypes
[22.05] Add CASTEP datatypes
This commit is contained in:
John Chilton
@@ -8,6 +8,7 @@ The following individuals have contributed code to Galaxy:
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* Guruprasad Ananda <gua110@bx.psu.edu>
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* Evgeny Anatskiy <evgeny.anatskiy@gmail.com>
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* Florent Angly <florent.angly@gmail.com>
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* Patrick Austin <patrick.austin@stfc.ac.uk>
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* Raj Ayyampalayam <raj76@uga.edu>
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* Abdulrahman Azab <eng.azab@gmail.com>
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* Finn Bacall <finn.bacall@cs.man.ac.uk>
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@@ -34,6 +35,7 @@ The following individuals have contributed code to Galaxy:
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* Richard Burhans <burhans@bx.psu.edu>
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* Jennifer Cabral <jencabral@gmail.com>
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* Martin Čech <marten@bx.psu.edu>
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* Eli Chadwick <eli.chadwick@stfc.ac.uk>
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* Ramkrishna Chakrabarty <rc@bx.psu.edu>
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* Matt Chambers <matt.chambers42@gmail.com>
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* Brad Chapman <chapmanb@50mail.com>
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@@ -925,6 +925,10 @@
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<!-- Povray script -->
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<datatype extension="pov" type="galaxy.datatypes.text:Text" subclass="true" display_in_upload="true"/>
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<!-- End Structural Materials datatypes -->
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<!-- CASTEP types -->
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<datatype extension="castep" type="galaxy.datatypes.text:Castep" display_in_upload="true"/>
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<datatype extension="param" type="galaxy.datatypes.text:Param" display_in_upload="true"/>
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<datatype extension="den_fmt" type="galaxy.datatypes.text:FormattedDensity" display_in_upload="true"/>
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</registration>
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<sniffers>
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<!--
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@@ -1176,6 +1180,9 @@
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<sniffer type="galaxy.datatypes.media:Mpg"/>
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<sniffer type="galaxy.datatypes.speech:TextGrid" />
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<sniffer type="galaxy.datatypes.speech:BPF" />
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<sniffer type="galaxy.datatypes.text:Castep" />
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<sniffer type="galaxy.datatypes.text:FormattedDensity" />
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<sniffer type="galaxy.datatypes.text:Param" />
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<sniffer type="galaxy.datatypes.text:Yaml" />
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<!--
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Keep this commented until the sniff method in the assembly.py
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@@ -401,6 +401,15 @@ def guess_ext(fname_or_file_prefix: Union[str, "FilePrefix"], sniff_order, is_bi
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>>> fname = get_test_fname('Si.extxyz')
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>>> guess_ext(fname, sniff_order)
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'extxyz'
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>>> fname = get_test_fname('Si.castep')
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>>> guess_ext(fname, sniff_order)
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'castep'
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>>> fname = get_test_fname('Si.param')
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>>> guess_ext(fname, sniff_order)
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'param'
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>>> fname = get_test_fname('Si.den_fmt')
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>>> guess_ext(fname, sniff_order)
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'den_fmt'
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>>> fname = get_test_fname('mothur_datatypetest_true.mothur.otu')
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>>> guess_ext(fname, sniff_order)
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'mothur.otu'
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@@ -0,0 +1,925 @@
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+-------------------------------------------------+
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| |
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| CCC AA SSS TTTTT EEEEE PPPP |
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| C A A S T E P P |
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| C AAAA SS T EEE PPPP |
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| C A A S T E P |
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| CCC A A SSS T EEEEE P |
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| |
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+-------------------------------------------------+
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| |
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| Welcome to Academic Release CASTEP version 18.1 |
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| Ab Initio Total Energy Program |
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| |
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| Authors: |
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| M. Segall, M. Probert, C. Pickard, P. Hasnip, |
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| S. Clark, K. Refson, J. R. Yates, M. Payne |
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| |
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| Contributors: |
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| P. Lindan, P. Haynes, J. White, V. Milman, |
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| N. Govind, M. Gibson, P. Tulip, V. Cocula, |
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| B. Montanari, D. Quigley, M. Glover, |
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| L. Bernasconi, A. Perlov, M. Plummer, |
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| E. McNellis, J. Meyer, J. Gale, D. Jochym |
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| J. Aarons, B. Walker, R. Gillen, D. Jones |
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| T. Green, I. J. Bush, C. J. Armstrong, |
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| E. J. Higgins, E. L. Brown, M. S. McFly, |
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| J. Wilkins, B-C. Shih, P. J. P. Byrne |
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| |
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| Copyright (c) 2000 - 2017 |
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| |
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| Distributed under the terms of an |
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| Agreement between the United Kingdom |
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| Car-Parrinello (UKCP) Consortium, |
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| Daresbury Laboratory and Accelrys, Inc. |
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| |
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| Please cite |
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| |
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| "First principles methods using CASTEP" |
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| |
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| Zeitschrift fuer Kristallographie |
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| 220(5-6) pp. 567-570 (2005) |
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| |
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| S. J. Clark, M. D. Segall, C. J. Pickard, |
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| P. J. Hasnip, M. J. Probert, K. Refson, |
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| M. C. Payne |
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| |
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| in all publications arising from |
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| your use of CASTEP |
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| |
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+-------------------------------------------------+
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Compiled for linux_x86_64_ifort17 on Wed, 28 Feb 2018 17:00:19 +0000
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from code version baee3ec33e17+ Mon, 11 Dec 2017 11:05:17 +0000
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Compiler: Intel Fortran 17.0.2.174; Optimisation: fast
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MATHLIBS: Intel MKL(2017.0.2) (LAPACK version 3.7.0)
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FFT Lib : mkl
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Fundamental constants values: CODATA 2014
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Run started: Mon, 06 Sep 2021 11:25:23 +0100
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Atomic calculation performed for Si: 1s2 2s2 2p6 3s2 3p2
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Converged in 54 iterations to an ae energy of -7886.857 eV
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============================================================
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| Pseudopotential Report - Date of generation 6-09-2021 |
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------------------------------------------------------------
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| Element: Si Ionic charge: 4.00 Level of theory: PBE |
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| Atomic Solver: Koelling-Harmon |
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| |
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| Reference Electronic Structure |
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| Orbital Occupation Energy |
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| 3s 2.000 -0.397 |
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| 3p 2.000 -0.150 |
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| |
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| Pseudopotential Definition |
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| Beta l e Rc scheme norm |
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| 1 0 -0.397 1.797 qc 0 |
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| 2 0 0.250 1.797 qc 0 |
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| 3 1 -0.150 1.797 qc 0 |
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| 4 1 0.250 1.797 qc 0 |
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| 5 2 0.000 1.797 qc 0 |
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| 6 2 0.250 1.797 qc 0 |
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| loc 3 0.000 1.797 pn 0 |
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| |
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| Augmentation charge Rinner = 1.255 |
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| Partial core correction Rc = 1.255 |
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------------------------------------------------------------
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| "3|1.8|5|6|7|30:31:32" |
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------------------------------------------------------------
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| Author: Chris J. Pickard, Cambridge University |
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============================================================
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Pseudo atomic calculation performed for Si 3s2 3p2
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Converged in 23 iterations to a total energy of -165.0674 eV
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Calculation not parallelised.
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************************************ Title ************************************
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***************************** General Parameters ******************************
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output verbosity : normal (1)
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write checkpoint data to : Si.check
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type of calculation : geometry optimization
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stress calculation : off
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density difference calculation : off
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electron localisation func (ELF) calculation : off
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Hirshfeld analysis : off
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unlimited duration calculation
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timing information : on
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memory usage estimate : on
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write extra output files : on
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write final potential to formatted file : off
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write final density to formatted file : on
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write structure in CELL formatted file : on
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write BibTeX reference list : on
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write OTFG pseudopotential files : on
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write electrostatic potential file : on
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write bands file : on
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checkpoint writing : both castep_bin and check files
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output length unit : A
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output mass unit : amu
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output time unit : ps
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output charge unit : e
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output spin unit : hbar/2
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output energy unit : eV
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output force unit : eV/A
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output velocity unit : A/ps
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output pressure unit : GPa
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output inv_length unit : 1/A
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output frequency unit : cm-1
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output force constant unit : eV/A**2
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output volume unit : A**3
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output IR intensity unit : (D/A)**2/amu
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output dipole unit : D
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output efield unit : eV/A/e
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output entropy unit : J/mol/K
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wavefunctions paging : none
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random number generator seed : randomised (112523545)
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data distribution : optimal for this architecture
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optimization strategy : maximize speed(+++)
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*********************** Exchange-Correlation Parameters ***********************
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using functional : Perdew Burke Ernzerhof
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relativistic treatment : Koelling-Harmon
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DFT+D: Semi-empirical dispersion correction : off
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************************* Pseudopotential Parameters **************************
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pseudopotential representation : reciprocal space
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<beta|phi> representation : reciprocal space
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spin-orbit coupling : off
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**************************** Basis Set Parameters *****************************
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plane wave basis set cut-off : 450.0000 eV
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size of standard grid : 1.7500
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size of fine gmax : 19.0188 1/A
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finite basis set correction : automatic
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number of sample energies : 3
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sample spacing : 5.0000 eV
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**************************** Electronic Parameters ****************************
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number of electrons : 32.00
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net charge of system : 0.000
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treating system as non-spin-polarized
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number of bands : 20
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********************* Electronic Minimization Parameters **********************
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Method: Treating system as metallic with density mixing treatment of electrons,
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and number of SD steps : 1
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and number of CG steps : 4
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total energy / atom convergence tol. : 0.1000E-08 eV
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eigen-energy convergence tolerance : 0.5000E-09 eV
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max force / atom convergence tol. : ignored
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convergence tolerance window : 3 cycles
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max. number of SCF cycles : 100
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number of fixed-spin iterations : 10
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smearing scheme : Gaussian
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smearing width : 0.2000 eV
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Fermi energy convergence tolerance : 0.2721E-13 eV
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periodic dipole correction : NONE
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************************** Density Mixing Parameters **************************
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density-mixing scheme : Broyden
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max. length of mixing history : 20
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charge density mixing amplitude : 0.8000
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cut-off energy for mixing : 450.0 eV
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*********************** Population Analysis Parameters ************************
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Population analysis with cutoff : 3.000 A
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Population analysis output : summary and pdos components
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********************** Geometry Optimization Parameters ***********************
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optimization method : LBFGS
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max. no. of LBFGS updates : unbounded
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variable cell method : fixed basis quality
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max. number of steps : 100
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estimated bulk modulus : 500.0 GPa
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estimated <frequency> : 1668. cm-1
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geom line minimiser : on
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with line minimiser tolerance : 0.4000
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total energy convergence tolerance : 0.2000E-04 eV/atom
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max ionic |force| tolerance : 0.5000E-01 eV/A
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max ionic |displacement| tolerance : 0.1000E-02 A
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max |stress component| tolerance : 0.1000 GPa
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convergence tolerance window : 2 steps
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backup results every : 3600 seconds
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write geom trajectory file : on
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*******************************************************************************
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-------------------------------
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Unit Cell
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-------------------------------
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Real Lattice(A) Reciprocal Lattice(1/A)
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5.3810000 0.0000000 0.0000000 1.167661272 0.000000000 0.000000000
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0.0000000 5.3810000 0.0000000 0.000000000 1.167661272 0.000000000
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0.0000000 0.0000000 5.3810000 0.000000000 0.000000000 1.167661272
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Lattice parameters(A) Cell Angles
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a = 5.381000 alpha = 90.000000
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b = 5.381000 beta = 90.000000
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c = 5.381000 gamma = 90.000000
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Current cell volume = 155.807721 A**3
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density = 1.442059 AMU/A**3
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= 2.394596 g/cm^3
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-------------------------------
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Cell Contents
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-------------------------------
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Total number of ions in cell = 8
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Total number of species in cell = 1
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Max number of any one species = 8
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xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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x Element Atom Fractional coordinates of atoms x
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x Number u v w x
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x----------------------------------------------------------x
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x Si 1 0.000000 0.000000 0.000000 x
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x Si 2 0.750000 0.750000 0.250000 x
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x Si 3 0.500000 0.000000 0.500000 x
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x Si 4 0.750000 0.250000 0.750000 x
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x Si 5 0.000000 0.500000 0.500000 x
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x Si 6 0.250000 0.250000 0.250000 x
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x Si 7 0.250000 0.750000 0.750000 x
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x Si 8 0.500000 0.500000 0.000000 x
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xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
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No user defined ionic velocities
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-------------------------------
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Details of Species
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-------------------------------
|
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|
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Mass of species in AMU
|
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Si 28.0855000
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Electric Quadrupole Moment (Barn)
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Si 1.0000000 No Isotope Defined
|
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|
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Files used for pseudopotentials:
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Si 3|1.8|5|6|7|30:31:32
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|
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-------------------------------
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k-Points For BZ Sampling
|
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-------------------------------
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MP grid size for SCF calculation is 2 2 2
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with an offset of 0.000 0.000 0.000
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Number of kpoints used = 1
|
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|
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-------------------------------
|
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Symmetry and Constraints
|
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-------------------------------
|
||||
|
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Cell is a supercell containing 4 primitive cells
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Maximum deviation from symmetry = 0.00000 ANG
|
||||
|
||||
Number of symmetry operations = 192
|
||||
Number of ionic constraints = 3
|
||||
Point group of crystal = 32: Oh, m-3m, 4/m -3 2/m
|
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Space group of crystal = 227: Fd-3m, F 4d 2 3 -1d
|
||||
|
||||
Set iprint > 1 for details on symmetry rotations/translations
|
||||
|
||||
Centre of mass is constrained
|
||||
Set iprint > 1 for details of linear ionic constraints
|
||||
|
||||
Number of cell constraints= 5
|
||||
Cell constraints are: 1 1 1 0 0 0
|
||||
|
||||
External pressure/stress (GPa)
|
||||
0.00000 0.00000 0.00000
|
||||
0.00000 0.00000
|
||||
0.00000
|
||||
|
||||
+---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+
|
||||
| Memory Disk |
|
||||
| Baseline code, static data and system overhead 147.0 MB 0.0 MB |
|
||||
| BLAS internal memory storage 0.0 MB 0.0 MB |
|
||||
| Model and support data 96.5 MB 0.0 MB |
|
||||
| Electronic energy minimisation requirements 18.1 MB 0.0 MB |
|
||||
| Force calculation requirements 6.8 MB 0.0 MB |
|
||||
| ----------------------------- |
|
||||
| Approx. total storage required per process 261.6 MB 0.0 MB |
|
||||
| |
|
||||
| Requirements will fluctuate during execution and may exceed these estimates |
|
||||
+-----------------------------------------------------------------------------+
|
||||
Calculating finite basis set correction with 3 cut-off energies.
|
||||
Finite basis spacing too small - increasing from 5.000 eV to 5.500 eV.
|
||||
Calculating total energy with cut-off of 439.000 eV.
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
SCF loop Energy Fermi Energy gain Timer <-- SCF
|
||||
energy per atom (sec) <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
Initial -5.64101230E+001 0.00000000E+000 4.47 <-- SCF
|
||||
1 -1.26087137E+003 7.30782707E+000 1.50557656E+002 4.68 <-- SCF
|
||||
2 -1.35938629E+003 4.66581032E+000 1.23143640E+001 4.82 <-- SCF
|
||||
3 -1.36377374E+003 4.76579695E+000 5.48431567E-001 4.92 <-- SCF
|
||||
4 -1.36313460E+003 4.91722518E+000 -7.98919709E-002 5.16 <-- SCF
|
||||
5 -1.36310173E+003 5.01437495E+000 -4.10929548E-003 5.39 <-- SCF
|
||||
6 -1.36310836E+003 5.02981306E+000 8.29406823E-004 5.63 <-- SCF
|
||||
7 -1.36310970E+003 5.04087673E+000 1.67179288E-004 5.85 <-- SCF
|
||||
8 -1.36310971E+003 5.04130088E+000 1.52437545E-006 6.10 <-- SCF
|
||||
9 -1.36310971E+003 5.04144672E+000 1.03787821E-007 6.32 <-- SCF
|
||||
10 -1.36310971E+003 5.04145497E+000 1.54362213E-009 6.50 <-- SCF
|
||||
11 -1.36310971E+003 5.04146302E+000 -1.02958090E-011 6.68 <-- SCF
|
||||
12 -1.36310971E+003 5.04145707E+000 1.25894059E-010 6.85 <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
|
||||
Final energy, E = -1363.109714972 eV
|
||||
Final free energy (E-TS) = -1363.109714972 eV
|
||||
(energies not corrected for finite basis set)
|
||||
|
||||
NB est. 0K energy (E-0.5TS) = -1363.109714972 eV
|
||||
|
||||
Calculating total energy with cut-off of 444.500 eV.
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
SCF loop Energy Fermi Energy gain Timer <-- SCF
|
||||
energy per atom (sec) <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
Initial -1.36310971E+003 0.00000000E+000 7.11 <-- SCF
|
||||
1 -1.36310978E+003 5.04145634E+000 7.60888708E-006 7.23 <-- SCF
|
||||
2 -1.36310978E+003 5.04145634E+000 2.13360099E-009 7.44 <-- SCF
|
||||
3 -1.36310978E+003 5.04145364E+000 1.09765892E-008 7.61 <-- SCF
|
||||
4 -1.36310978E+003 5.04145382E+000 4.52193867E-010 7.78 <-- SCF
|
||||
5 -1.36310978E+003 5.04145384E+000 1.62412762E-011 7.96 <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
|
||||
Final energy, E = -1363.109775952 eV
|
||||
Final free energy (E-TS) = -1363.109775952 eV
|
||||
(energies not corrected for finite basis set)
|
||||
|
||||
NB est. 0K energy (E-0.5TS) = -1363.109775952 eV
|
||||
|
||||
Calculating total energy with cut-off of 450.000 eV.
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
SCF loop Energy Fermi Energy gain Timer <-- SCF
|
||||
energy per atom (sec) <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
Initial -1.36310978E+003 0.00000000E+000 8.21 <-- SCF
|
||||
1 -1.36310985E+003 5.04145272E+000 9.67300632E-006 8.34 <-- SCF
|
||||
2 -1.36310985E+003 5.04145272E+000 2.84176414E-009 8.54 <-- SCF
|
||||
3 -1.36310985E+003 5.04144793E+000 1.36981147E-008 8.72 <-- SCF
|
||||
4 -1.36310985E+003 5.04144740E+000 5.93072437E-010 8.90 <-- SCF
|
||||
5 -1.36310985E+003 5.04144750E+000 1.82472672E-011 9.07 <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
|
||||
Final energy, E = -1363.109853474 eV
|
||||
Final free energy (E-TS) = -1363.109853474 eV
|
||||
(energies not corrected for finite basis set)
|
||||
|
||||
NB est. 0K energy (E-0.5TS) = -1363.109853474 eV
|
||||
|
||||
For future reference: finite basis dEtot/dlog(Ecut) = -0.004949eV
|
||||
Total energy corrected for finite basis set = -1363.109854 eV
|
||||
|
||||
+---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+
|
||||
| Memory Disk |
|
||||
| Model and support data 107.3 MB 0.0 MB |
|
||||
| Electronic energy minimisation requirements 18.1 MB 0.0 MB |
|
||||
| Geometry minimisation requirements 20.1 MB 0.0 MB |
|
||||
| ----------------------------- |
|
||||
| Approx. total storage required per process 145.5 MB 0.0 MB |
|
||||
| |
|
||||
| Requirements will fluctuate during execution and may exceed these estimates |
|
||||
+-----------------------------------------------------------------------------+
|
||||
|
||||
|
||||
*********** Symmetrised Stress Tensor ***********
|
||||
* *
|
||||
* Cartesian components (GPa) *
|
||||
* --------------------------------------------- *
|
||||
* x y z *
|
||||
* *
|
||||
* x -5.177024 0.000000 -0.000000 *
|
||||
* y 0.000000 -5.177024 0.000000 *
|
||||
* z -0.000000 0.000000 -5.177024 *
|
||||
* *
|
||||
* Pressure: 5.1770 *
|
||||
* *
|
||||
*************************************************
|
||||
LBFGS: finished iteration 0 with enthalpy= -1.36310985E+003 eV
|
||||
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
| Parameter | value | tolerance | units | OK? | <-- LBFGS
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
| dE/ion | 0.000000E+000 | 2.000000E-005 | eV | No | <-- LBFGS
|
||||
| Smax | 5.177024E+000 | 1.000000E-001 | GPa | No | <-- LBFGS
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
|
||||
|
||||
================================================================================
|
||||
Starting LBFGS iteration 1 ...
|
||||
================================================================================
|
||||
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| Step | lambda | F.delta' | enthalpy | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| previous | 0.000000 | 0.320456 | -1363.109854 | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
LBFGS: starting iteration 1 with trial guess (lambda= 1.000000)
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
+---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+
|
||||
| Memory Disk |
|
||||
| Model and support data 107.4 MB 0.0 MB |
|
||||
| Electronic energy minimisation requirements 18.3 MB 0.0 MB |
|
||||
| Geometry minimisation requirements 20.2 MB 0.0 MB |
|
||||
| ----------------------------- |
|
||||
| Approx. total storage required per process 145.9 MB 0.0 MB |
|
||||
| |
|
||||
| Requirements will fluctuate during execution and may exceed these estimates |
|
||||
+-----------------------------------------------------------------------------+
|
||||
|
||||
|
||||
-------------------------------
|
||||
Unit Cell
|
||||
-------------------------------
|
||||
Real Lattice(A) Reciprocal Lattice(1/A)
|
||||
5.3995717 0.0000000 0.0000000 1.163645127 -0.000000000 -0.000000000
|
||||
0.0000000 5.3995717 -0.0000000 -0.000000000 1.163645127 0.000000000
|
||||
0.0000000 -0.0000000 5.3995717 -0.000000000 0.000000000 1.163645127
|
||||
|
||||
Lattice parameters(A) Cell Angles
|
||||
a = 5.399572 alpha = 90.000000
|
||||
b = 5.399572 beta = 90.000000
|
||||
c = 5.399572 gamma = 90.000000
|
||||
|
||||
Current cell volume = 157.426536 A**3
|
||||
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
SCF loop Energy Fermi Energy gain Timer <-- SCF
|
||||
energy per atom (sec) <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
Initial -1.36314744E+003 0.00000000E+000 12.34 <-- SCF
|
||||
1 -1.36315844E+003 4.95156616E+000 1.37486053E-003 12.47 <-- SCF
|
||||
2 -1.36315851E+003 4.95155282E+000 9.35306807E-006 12.73 <-- SCF
|
||||
3 -1.36315662E+003 4.95776926E+000 -2.35941488E-004 12.95 <-- SCF
|
||||
4 -1.36315648E+003 4.96110080E+000 -1.85388820E-005 13.16 <-- SCF
|
||||
5 -1.36315648E+003 4.96155240E+000 8.59711342E-007 13.41 <-- SCF
|
||||
6 -1.36315648E+003 4.96186437E+000 1.60128011E-007 13.62 <-- SCF
|
||||
7 -1.36315648E+003 4.96188331E+000 2.46968907E-009 13.81 <-- SCF
|
||||
8 -1.36315648E+003 4.96190061E+000 5.22137696E-010 13.99 <-- SCF
|
||||
9 -1.36315648E+003 4.96190086E+000 3.14916413E-011 14.16 <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
|
||||
Final energy, E = -1363.156484284 eV
|
||||
Final free energy (E-TS) = -1363.156484284 eV
|
||||
(energies not corrected for finite basis set)
|
||||
|
||||
NB est. 0K energy (E-0.5TS) = -1363.156484284 eV
|
||||
|
||||
|
||||
*********** Symmetrised Stress Tensor ***********
|
||||
* *
|
||||
* Cartesian components (GPa) *
|
||||
* --------------------------------------------- *
|
||||
* x y z *
|
||||
* *
|
||||
* x -4.061235 0.000000 0.000000 *
|
||||
* y 0.000000 -4.061235 0.000000 *
|
||||
* z 0.000000 0.000000 -4.061235 *
|
||||
* *
|
||||
* Pressure: 4.0612 *
|
||||
* *
|
||||
*************************************************
|
||||
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| Step | lambda | F.delta' | enthalpy | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| previous | 0.000000 | 0.320456 | -1363.109854 | <-- min LBFGS
|
||||
| trial step | 1.000000 | 0.253127 | -1363.156472 | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
LBFGS: improving iteration 1 with line minimization (lambda= 4.759574)
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
+---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+
|
||||
| Memory Disk |
|
||||
| Model and support data 107.8 MB 0.0 MB |
|
||||
| Electronic energy minimisation requirements 18.8 MB 0.0 MB |
|
||||
| Geometry minimisation requirements 20.9 MB 0.0 MB |
|
||||
| ----------------------------- |
|
||||
| Approx. total storage required per process 147.5 MB 0.0 MB |
|
||||
| |
|
||||
| Requirements will fluctuate during execution and may exceed these estimates |
|
||||
+-----------------------------------------------------------------------------+
|
||||
|
||||
|
||||
-------------------------------
|
||||
Unit Cell
|
||||
-------------------------------
|
||||
Real Lattice(A) Reciprocal Lattice(1/A)
|
||||
5.4693934 0.0000000 0.0000000 1.148790150 -0.000000000 -0.000000000
|
||||
0.0000000 5.4693934 -0.0000000 -0.000000000 1.148790150 0.000000000
|
||||
0.0000000 -0.0000000 5.4693934 -0.000000000 0.000000000 1.148790150
|
||||
|
||||
Lattice parameters(A) Cell Angles
|
||||
a = 5.469393 alpha = 90.000000
|
||||
b = 5.469393 beta = 90.000000
|
||||
c = 5.469393 gamma = 90.000000
|
||||
|
||||
Current cell volume = 163.612882 A**3
|
||||
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
SCF loop Energy Fermi Energy gain Timer <-- SCF
|
||||
energy per atom (sec) <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
Initial -1.36311283E+003 0.00000000E+000 17.37 <-- SCF
|
||||
1 -1.36326554E+003 4.62795268E+000 1.90884917E-002 17.50 <-- SCF
|
||||
2 -1.36326661E+003 4.62774625E+000 1.34437820E-004 17.77 <-- SCF
|
||||
3 -1.36324018E+003 4.65185039E+000 -3.30422824E-003 17.99 <-- SCF
|
||||
4 -1.36323803E+003 4.66500872E+000 -2.69161578E-004 18.22 <-- SCF
|
||||
5 -1.36323813E+003 4.66680663E+000 1.33542573E-005 18.47 <-- SCF
|
||||
6 -1.36323815E+003 4.66809170E+000 2.60192786E-006 18.69 <-- SCF
|
||||
7 -1.36323815E+003 4.66816703E+000 4.10755652E-008 18.92 <-- SCF
|
||||
8 -1.36323815E+003 4.66823094E+000 7.59506849E-009 19.12 <-- SCF
|
||||
9 -1.36323815E+003 4.66823522E+000 9.19855616E-011 19.30 <-- SCF
|
||||
10 -1.36323815E+003 4.66823439E+000 2.25492719E-011 19.47 <-- SCF
|
||||
11 -1.36323815E+003 4.66823444E+000 5.36542162E-012 19.65 <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
|
||||
Final energy, E = -1363.238153587 eV
|
||||
Final free energy (E-TS) = -1363.238153587 eV
|
||||
(energies not corrected for finite basis set)
|
||||
|
||||
NB est. 0K energy (E-0.5TS) = -1363.238153587 eV
|
||||
|
||||
|
||||
*********** Symmetrised Stress Tensor ***********
|
||||
* *
|
||||
* Cartesian components (GPa) *
|
||||
* --------------------------------------------- *
|
||||
* x y z *
|
||||
* *
|
||||
* x -0.296550 0.000000 0.000000 *
|
||||
* y 0.000000 -0.296550 0.000000 *
|
||||
* z 0.000000 0.000000 -0.296550 *
|
||||
* *
|
||||
* Pressure: 0.2966 *
|
||||
* *
|
||||
*************************************************
|
||||
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| Step | lambda | F.delta' | enthalpy | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| previous | 0.000000 | 0.320456 | -1363.109854 | <-- min LBFGS
|
||||
| trial step | 1.000000 | 0.253127 | -1363.156472 | <-- min LBFGS
|
||||
| line step | 4.759574 | 0.018964 | -1363.238141 | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
|
||||
LBFGS: finished iteration 1 with enthalpy= -1.36323814E+003 eV
|
||||
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
| Parameter | value | tolerance | units | OK? | <-- LBFGS
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
| dE/ion | 1.603591E-002 | 2.000000E-005 | eV | No | <-- LBFGS
|
||||
| Smax | 2.965505E-001 | 1.000000E-001 | GPa | No | <-- LBFGS
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
|
||||
|
||||
================================================================================
|
||||
Starting LBFGS iteration 2 ...
|
||||
================================================================================
|
||||
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| Step | lambda | F.delta' | enthalpy | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| previous | 0.000000 | 0.018964 | -1363.238141 | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
LBFGS: starting iteration 2 with trial guess (lambda= 1.000000)
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
-------------------------------
|
||||
Unit Cell
|
||||
-------------------------------
|
||||
Real Lattice(A) Reciprocal Lattice(1/A)
|
||||
5.4749536 0.0000000 0.0000000 1.147623490 -0.000000000 -0.000000000
|
||||
0.0000000 5.4749536 -0.0000000 -0.000000000 1.147623490 0.000000000
|
||||
0.0000000 -0.0000000 5.4749536 -0.000000000 0.000000000 1.147623490
|
||||
|
||||
Lattice parameters(A) Cell Angles
|
||||
a = 5.474954 alpha = 90.000000
|
||||
b = 5.474954 beta = 90.000000
|
||||
c = 5.474954 gamma = 90.000000
|
||||
|
||||
Current cell volume = 164.112370 A**3
|
||||
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
SCF loop Energy Fermi Energy gain Timer <-- SCF
|
||||
energy per atom (sec) <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
Initial -1.36323784E+003 0.00000000E+000 22.87 <-- SCF
|
||||
1 -1.36323882E+003 4.64196095E+000 1.21622452E-004 23.00 <-- SCF
|
||||
2 -1.36323882E+003 4.64195965E+000 8.22711951E-007 23.26 <-- SCF
|
||||
3 -1.36323866E+003 4.64389061E+000 -2.08140999E-005 23.47 <-- SCF
|
||||
4 -1.36323864E+003 4.64494525E+000 -1.70615912E-006 23.70 <-- SCF
|
||||
5 -1.36323864E+003 4.64508950E+000 8.51569025E-008 23.94 <-- SCF
|
||||
6 -1.36323864E+003 4.64519280E+000 1.66869446E-008 24.16 <-- SCF
|
||||
7 -1.36323864E+003 4.64519906E+000 2.66893473E-010 24.34 <-- SCF
|
||||
8 -1.36323864E+003 4.64520368E+000 6.32249682E-011 24.52 <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
|
||||
Final energy, E = -1363.238642637 eV
|
||||
Final free energy (E-TS) = -1363.238642637 eV
|
||||
(energies not corrected for finite basis set)
|
||||
|
||||
NB est. 0K energy (E-0.5TS) = -1363.238642637 eV
|
||||
|
||||
|
||||
*********** Symmetrised Stress Tensor ***********
|
||||
* *
|
||||
* Cartesian components (GPa) *
|
||||
* --------------------------------------------- *
|
||||
* x y z *
|
||||
* *
|
||||
* x -0.024309 -0.000000 -0.000000 *
|
||||
* y -0.000000 -0.024309 -0.000000 *
|
||||
* z -0.000000 -0.000000 -0.024309 *
|
||||
* *
|
||||
* Pressure: 0.0243 *
|
||||
* *
|
||||
*************************************************
|
||||
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| Step | lambda | F.delta' | enthalpy | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| previous | 0.000000 | 0.018964 | -1363.238141 | <-- min LBFGS
|
||||
| trial step | 1.000000 | 0.001558 | -1363.238640 | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
|
||||
LBFGS: finished iteration 2 with enthalpy= -1.36323864E+003 eV
|
||||
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
| Parameter | value | tolerance | units | OK? | <-- LBFGS
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
| dE/ion | 6.238857E-005 | 2.000000E-005 | eV | No | <-- LBFGS
|
||||
| Smax | 2.430886E-002 | 1.000000E-001 | GPa | Yes | <-- LBFGS
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
|
||||
|
||||
================================================================================
|
||||
Starting LBFGS iteration 3 ...
|
||||
================================================================================
|
||||
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| Step | lambda | F.delta' | enthalpy | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| previous | 0.000000 | 0.001558 | -1363.238640 | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
|
||||
|
||||
--------------------------------------------------------------------------------
|
||||
LBFGS: starting iteration 3 with trial guess (lambda= 1.000000)
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
+---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+
|
||||
| Memory Disk |
|
||||
| Model and support data 107.8 MB 0.0 MB |
|
||||
| Electronic energy minimisation requirements 18.9 MB 0.0 MB |
|
||||
| Geometry minimisation requirements 20.9 MB 0.0 MB |
|
||||
| ----------------------------- |
|
||||
| Approx. total storage required per process 147.6 MB 0.0 MB |
|
||||
| |
|
||||
| Requirements will fluctuate during execution and may exceed these estimates |
|
||||
+-----------------------------------------------------------------------------+
|
||||
|
||||
|
||||
-------------------------------
|
||||
Unit Cell
|
||||
-------------------------------
|
||||
Real Lattice(A) Reciprocal Lattice(1/A)
|
||||
5.4754511 0.0000000 0.0000000 1.147519202 -0.000000000 -0.000000000
|
||||
0.0000000 5.4754511 -0.0000000 -0.000000000 1.147519202 0.000000000
|
||||
0.0000000 -0.0000000 5.4754511 -0.000000000 0.000000000 1.147519202
|
||||
|
||||
Lattice parameters(A) Cell Angles
|
||||
a = 5.475451 alpha = 90.000000
|
||||
b = 5.475451 beta = 90.000000
|
||||
c = 5.475451 gamma = 90.000000
|
||||
|
||||
Current cell volume = 164.157119 A**3
|
||||
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
SCF loop Energy Fermi Energy gain Timer <-- SCF
|
||||
energy per atom (sec) <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
Initial -1.36323864E+003 0.00000000E+000 27.72 <-- SCF
|
||||
1 -1.36323865E+003 4.64285521E+000 1.46970545E-006 27.86 <-- SCF
|
||||
2 -1.36323865E+003 4.64285520E+000 7.45718682E-009 28.12 <-- SCF
|
||||
3 -1.36323865E+003 4.64302739E+000 -1.65330754E-007 28.34 <-- SCF
|
||||
4 -1.36323865E+003 4.64312213E+000 -1.37143802E-008 28.56 <-- SCF
|
||||
5 -1.36323865E+003 4.64313484E+000 6.68260845E-010 28.73 <-- SCF
|
||||
6 -1.36323865E+003 4.64314455E+000 1.38969254E-010 28.91 <-- SCF
|
||||
------------------------------------------------------------------------ <-- SCF
|
||||
|
||||
Final energy, E = -1363.238649135 eV
|
||||
Final free energy (E-TS) = -1363.238649135 eV
|
||||
(energies not corrected for finite basis set)
|
||||
|
||||
NB est. 0K energy (E-0.5TS) = -1363.238649135 eV
|
||||
|
||||
|
||||
*********** Symmetrised Stress Tensor ***********
|
||||
* *
|
||||
* Cartesian components (GPa) *
|
||||
* --------------------------------------------- *
|
||||
* x y z *
|
||||
* *
|
||||
* x -0.000125 0.000000 0.000000 *
|
||||
* y 0.000000 -0.000125 0.000000 *
|
||||
* z 0.000000 0.000000 -0.000125 *
|
||||
* *
|
||||
* Pressure: 0.0001 *
|
||||
* *
|
||||
*************************************************
|
||||
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| Step | lambda | F.delta' | enthalpy | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
| previous | 0.000000 | 0.001558 | -1363.238640 | <-- min LBFGS
|
||||
| trial step | 1.000000 | 8.002E-006 | -1363.238636 | <-- min LBFGS
|
||||
+------------+-------------+-------------+-----------------+ <-- min LBFGS
|
||||
|
||||
LBFGS: finished iteration 3 with enthalpy= -1.36323864E+003 eV
|
||||
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
| Parameter | value | tolerance | units | OK? | <-- LBFGS
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
| dE/ion | 4.633441E-007 | 2.000000E-005 | eV | Yes | <-- LBFGS
|
||||
| Smax | 1.248549E-004 | 1.000000E-001 | GPa | Yes | <-- LBFGS
|
||||
+-----------+-----------------+-----------------+------------+-----+ <-- LBFGS
|
||||
|
||||
LBFGS: Geometry optimization completed successfully.
|
||||
|
||||
================================================================================
|
||||
LBFGS: Final Configuration:
|
||||
================================================================================
|
||||
|
||||
-------------------------------
|
||||
Unit Cell
|
||||
-------------------------------
|
||||
Real Lattice(A) Reciprocal Lattice(1/A)
|
||||
5.4754511 0.0000000 0.0000000 1.147519202 -0.000000000 -0.000000000
|
||||
0.0000000 5.4754511 -0.0000000 -0.000000000 1.147519202 0.000000000
|
||||
0.0000000 -0.0000000 5.4754511 -0.000000000 0.000000000 1.147519202
|
||||
|
||||
Lattice parameters(A) Cell Angles
|
||||
a = 5.475451 alpha = 90.000000
|
||||
b = 5.475451 beta = 90.000000
|
||||
c = 5.475451 gamma = 90.000000
|
||||
|
||||
Current cell volume = 164.157119 A**3
|
||||
|
||||
LBFGS: Final Enthalpy = -1.36323864E+003 eV
|
||||
LBFGS: Final bulk modulus = 89.15153 GPa
|
||||
|
||||
******************************** Symmetrised Forces ********************************
|
||||
* *
|
||||
* Cartesian components (eV/A) *
|
||||
* -------------------------------------------------------------------------------- *
|
||||
* x y z *
|
||||
* *
|
||||
* Si 1 0.00000 0.00000 0.00000 *
|
||||
* Si 2 0.00000 0.00000 0.00000 *
|
||||
* Si 3 0.00000 0.00000 0.00000 *
|
||||
* Si 4 0.00000 0.00000 0.00000 *
|
||||
* Si 5 0.00000 0.00000 0.00000 *
|
||||
* Si 6 0.00000 0.00000 0.00000 *
|
||||
* Si 7 0.00000 0.00000 0.00000 *
|
||||
* Si 8 0.00000 0.00000 0.00000 *
|
||||
* *
|
||||
************************************************************************************
|
||||
|
||||
*********** Symmetrised Stress Tensor ***********
|
||||
* *
|
||||
* Cartesian components (GPa) *
|
||||
* --------------------------------------------- *
|
||||
* x y z *
|
||||
* *
|
||||
* x -0.000125 0.000000 0.000000 *
|
||||
* y 0.000000 -0.000125 0.000000 *
|
||||
* z 0.000000 0.000000 -0.000125 *
|
||||
* *
|
||||
* Pressure: 0.0001 *
|
||||
* *
|
||||
*************************************************
|
||||
|
||||
Pseudo atomic calculation performed for Si 3s2 3p2
|
||||
|
||||
Converged in 23 iterations to a total energy of -165.0674 eV
|
||||
|
||||
Charge spilling parameter for spin component 1 = 0.85%
|
||||
|
||||
Orbital Populations
|
||||
Ion Atom Orbital Charge
|
||||
-------------------------------------------
|
||||
Si 1 S 1.363
|
||||
Si 1 Px 0.879
|
||||
Si 1 Py 0.879
|
||||
Si 1 Pz 0.879
|
||||
Si 2 S 1.363
|
||||
Si 2 Px 0.879
|
||||
Si 2 Py 0.879
|
||||
Si 2 Pz 0.879
|
||||
Si 3 S 1.363
|
||||
Si 3 Px 0.879
|
||||
Si 3 Py 0.879
|
||||
Si 3 Pz 0.879
|
||||
Si 4 S 1.363
|
||||
Si 4 Px 0.879
|
||||
Si 4 Py 0.879
|
||||
Si 4 Pz 0.879
|
||||
Si 5 S 1.362
|
||||
Si 5 Px 0.879
|
||||
Si 5 Py 0.879
|
||||
Si 5 Pz 0.879
|
||||
Si 6 S 1.363
|
||||
Si 6 Px 0.879
|
||||
Si 6 Py 0.879
|
||||
Si 6 Pz 0.879
|
||||
Si 7 S 1.363
|
||||
Si 7 Px 0.879
|
||||
Si 7 Py 0.879
|
||||
Si 7 Pz 0.879
|
||||
Si 8 S 1.362
|
||||
Si 8 Px 0.879
|
||||
Si 8 Py 0.879
|
||||
Si 8 Pz 0.879
|
||||
-------------------------------------------
|
||||
Total: 32.000
|
||||
-------------------------------------------
|
||||
|
||||
Atomic Populations (Mulliken)
|
||||
-----------------------------
|
||||
Species Ion s p d f Total Charge (e)
|
||||
=====================================================================
|
||||
Si 1 1.36 2.64 0.00 0.00 4.00 0.00
|
||||
Si 2 1.36 2.64 0.00 0.00 4.00 0.00
|
||||
Si 3 1.36 2.64 0.00 0.00 4.00 0.00
|
||||
Si 4 1.36 2.64 0.00 0.00 4.00 0.00
|
||||
Si 5 1.36 2.64 0.00 0.00 4.00 0.00
|
||||
Si 6 1.36 2.64 0.00 0.00 4.00 0.00
|
||||
Si 7 1.36 2.64 0.00 0.00 4.00 0.00
|
||||
Si 8 1.36 2.64 0.00 0.00 4.00 0.00
|
||||
=====================================================================
|
||||
|
||||
Bond Population Length (A)
|
||||
======================================================================
|
||||
Si 7 -- Si 8 0.74 2.37094
|
||||
Si 6 -- Si 8 0.74 2.37094
|
||||
Si 5 -- Si 7 0.74 2.37094
|
||||
Si 5 -- Si 6 0.74 2.37094
|
||||
Si 4 -- Si 8 0.74 2.37094
|
||||
Si 4 -- Si 5 0.74 2.37094
|
||||
Si 3 -- Si 7 0.74 2.37094
|
||||
Si 3 -- Si 6 0.74 2.37094
|
||||
Si 3 -- Si 4 0.74 2.37094
|
||||
Si 2 -- Si 8 0.74 2.37094
|
||||
Si 2 -- Si 5 0.74 2.37094
|
||||
Si 2 -- Si 3 0.74 2.37094
|
||||
Si 1 -- Si 7 0.74 2.37094
|
||||
Si 1 -- Si 6 0.74 2.37094
|
||||
Si 1 -- Si 4 0.74 2.37094
|
||||
Si 1 -- Si 2 0.74 2.37094
|
||||
======================================================================
|
||||
|
||||
|
||||
Writing analysis data to Si.castep_bin
|
||||
|
||||
Writing model to Si.check
|
||||
|
||||
A BibTeX formatted list of references used in this run has been written to
|
||||
Si.bib
|
||||
|
||||
Initialisation time = 3.71 s
|
||||
Calculation time = 28.61 s
|
||||
Finalisation time = 0.61 s
|
||||
Total time = 32.92 s
|
||||
Peak Memory Use = 416432 kB
|
||||
@@ -0,0 +1,13 @@
|
||||
BEGIN header
|
||||
|
||||
Real Lattice(A) Lattice parameters(A) Cell Angles
|
||||
5.4754511 0.0000000 0.0000000 a = 5.475451 alpha = 90.000000
|
||||
0.0000000 5.4754511 -0.0000000 b = 5.475451 beta = 90.000000
|
||||
0.0000000 -0.0000000 5.4754511 c = 5.475451 gamma = 90.000000
|
||||
|
||||
1 ! nspins
|
||||
1 1 1 ! fine FFT grid along <a,b,c>
|
||||
END header: data is "<a b c> charge" in units of electrons/grid_point * number
|
||||
of grid_points
|
||||
|
||||
1 1 1 220.238914
|
||||
@@ -0,0 +1,13 @@
|
||||
task : geometryoptimisation
|
||||
opt_strategy : speed
|
||||
num_dump_cycles : 0
|
||||
cutoff_energy : 450 eV
|
||||
elec_energy_tol : 1.0e-9 eV
|
||||
write_cell_structure : true
|
||||
max_scf_cycles : 100
|
||||
xc_functional : pbe
|
||||
geom_max_iter : 100
|
||||
geom_force_tol : 0.05
|
||||
backup_interval : 3600
|
||||
continuation : default
|
||||
write_formatted_density : true
|
||||
@@ -1091,3 +1091,110 @@ class Yaml(Text):
|
||||
except yaml.YAMLError:
|
||||
return False
|
||||
return False
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class Castep(Text):
|
||||
"""Report on a CASTEP calculation"""
|
||||
|
||||
file_ext = "castep"
|
||||
|
||||
def sniff_prefix(self, file_prefix: FilePrefix):
|
||||
"""Determines whether the file is a CASTEP log
|
||||
|
||||
>>> from galaxy.datatypes.sniff import get_test_fname
|
||||
>>> fname = get_test_fname('Si.castep')
|
||||
>>> Castep().sniff(fname)
|
||||
True
|
||||
>>> fname = get_test_fname('Si.param')
|
||||
>>> Castep().sniff(fname)
|
||||
False
|
||||
"""
|
||||
castep_header = [
|
||||
"+-------------------------------------------------+",
|
||||
"| |",
|
||||
"| CCC AA SSS TTTTT EEEEE PPPP |",
|
||||
"| C A A S T E P P |",
|
||||
"| C AAAA SS T EEE PPPP |",
|
||||
"| C A A S T E P |",
|
||||
"| CCC A A SSS T EEEEE P |",
|
||||
"| |",
|
||||
"+-------------------------------------------------+",
|
||||
]
|
||||
handle = file_prefix.string_io()
|
||||
for header_line in castep_header:
|
||||
if handle.readline().strip() != header_line:
|
||||
return False
|
||||
return True
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class Param(Yaml):
|
||||
"""CASTEP parameter input file"""
|
||||
|
||||
file_ext = "param"
|
||||
|
||||
def sniff_prefix(self, file_prefix: FilePrefix):
|
||||
"""
|
||||
Modified version of the normal Yaml sniff that also checks
|
||||
for a valid CASTEP task key-value pair, which is not case
|
||||
sensitive
|
||||
|
||||
>>> from galaxy.datatypes.sniff import get_test_fname
|
||||
>>> fname = get_test_fname('Si.param')
|
||||
>>> Param().sniff(fname)
|
||||
True
|
||||
>>> fname = get_test_fname('Si.castep')
|
||||
>>> Param().sniff(fname)
|
||||
False
|
||||
"""
|
||||
valid_tasks = [
|
||||
"SINGLEPOINT",
|
||||
"BANDSTRUCTURE",
|
||||
"GEOMETRYOPTIMIZATION",
|
||||
"GEOMETRYOPTIMISATION",
|
||||
"MOLECULARDYNAMICS",
|
||||
"OPTICS",
|
||||
"PHONON",
|
||||
"EFIELD",
|
||||
"PHONON+EFIELD",
|
||||
"TRANSITIONSTATESEARCH",
|
||||
"MAGRES",
|
||||
"ELNES",
|
||||
"ELECTRONICSPECTROSCOPY",
|
||||
]
|
||||
|
||||
# check it looks like YAML
|
||||
if not super().sniff_prefix(file_prefix):
|
||||
return False
|
||||
|
||||
# check the TASK keyword is present
|
||||
# and that it is set to a valid CASTEP task
|
||||
pattern = re.compile(r"^TASK ?: ?([A-Z\+]*)$", flags=re.IGNORECASE | re.MULTILINE)
|
||||
task = file_prefix.search(pattern)
|
||||
return task and task.group(1).upper() in valid_tasks
|
||||
|
||||
|
||||
@build_sniff_from_prefix
|
||||
class FormattedDensity(Text):
|
||||
"""Final electron density from a CASTEP calculation written to an ASCII file"""
|
||||
|
||||
file_ext = "den_fmt"
|
||||
|
||||
def sniff_prefix(self, file_prefix: FilePrefix):
|
||||
"""Determines whether the file contains electron densities in the CASTEP den_fmt format
|
||||
|
||||
>>> from galaxy.datatypes.sniff import get_test_fname
|
||||
>>> fname = get_test_fname('Si.den_fmt')
|
||||
>>> FormattedDensity().sniff(fname)
|
||||
True
|
||||
>>> fname = get_test_fname('Si.param')
|
||||
>>> FormattedDensity().sniff(fname)
|
||||
False
|
||||
"""
|
||||
begin_header = "BEGIN header"
|
||||
end_header = 'END header: data is "<a b c> charge" in units of electrons/grid_point * number'
|
||||
grid_points = "of grid_points"
|
||||
handle = file_prefix.string_io()
|
||||
lines = handle.readlines()
|
||||
return lines[0].strip() == begin_header and lines[9].strip() == end_header and lines[10].strip() == grid_points
|
||||
|
||||
Reference in New Issue
Block a user