Mercurial > repos > muon-spectroscopy-computational-project > pm_nq
changeset 0:16ef6bc73b17 draft
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_nq commit 4f06b404d8b7fb83995f3052faa7e2ec7811f507
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Fri, 03 Feb 2023 15:39:49 +0000 |
| parents | |
| children | f08b8c705e74 |
| files | muon_macros.xml pm_nq.xml test-data/Si.castep test-data/Si.cell test-data/Si.param test-data/Si.phonon test-data/averages.dat test-data/ethyleneMu_opt.phonons.pkl test-data/ethyleneMu_opt.xyz test-data/geo_end.gen test-data/submit.sh test-data/tree.txt test-data/tree_dftb.txt test-data/tree_extra_files.txt test-data/zipped_input.zip |
| diffstat | 15 files changed, 3463 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/muon_macros.xml Fri Feb 03 15:39:49 2023 +0000 @@ -0,0 +1,20 @@ +<macros> + <xml name="dftb_set"> + <param type="select" name="dftb_set" value="3ob-3-1" display="radio" label="DFTB parameter set" help="The parameter set to use for DFTB+. Currently supported are: 3ob-3-1 and pbc-0-3. See help section at the bottom of the page for details."> + <option value="3ob-3-1">3ob-3-1</option> + <option value="pbc-0-3">pbc-0-3</option> + </param> + </xml> + <xml name="dftb+"> + <expand macro="dftb_set"/> + <param type="boolean" name="dftb_pbc" label="Use periodic boundary conditions" help="Whether to turn on periodic boundary conditions in DFTB+." checked="true"/> + </xml> + <xml name="dftb_optionals"> + <param type="text" argument="dftb_optionals" value="[]" optional="true" label="DFTB optional files" help="Additional optional json files to activate for DFTBArgs (for example, dftd3.json will use DFTD3 dispersion forces for 3ob-3-1 if DFTB+ has been compiled to support them)."/> + </xml> + <xml name="k_points_grid"> + <param type="text" argument="k_points_grid" value="[1,1,1]" label="K-points grid" help="List of three integer k-points. Default is [1,1,1]."> + <validator type="regex" message="Input should only contain whitespace, '[', ']', ',' and digits.">^[\s\d,\[\]]+$</validator> + </param> + </xml> +</macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pm_nq.xml Fri Feb 03 15:39:49 2023 +0000 @@ -0,0 +1,332 @@ +<tool id="pm_nq" name="PyMuonSuite Quantum Averaging" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@" python_template_version="3.5" profile="22.05"> + <description>generate and average displaced structures</description> + <macros> + <!-- version of underlying tool (PEP 440) --> + <token name="@TOOL_VERSION@">0.2.3</token> + <!-- version of this tool wrapper (integer) --> + <token name="@WRAPPER_VERSION@">0</token> + <!-- citation should be updated with every underlying tool version --> + <!-- typical fields to update are version, month, year, and doi --> + <token name="@TOOL_CITATION@"> + @software{Sturniolo_pymuon-suite_2022, + author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and Mudaraddi, Anish and {Muon Spectroscopy Computational Project}}, + license = {GPL-3.0}, + month = {8}, + title = {{pymuon-suite}}, + url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite}, + version = {v0.2.3}, + doi = {10.5281/zenodo.7025644}, + year = {2022} + } + </token> + <import>muon_macros.xml</import> + </macros> + <creator> + <person givenName="Patrick" familyName="Austin" url="https://github.com/patrick-austin"/> + <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/> + </creator> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">pymuonsuite</requirement> + <requirement type="package" version="1.0.0">euphonic</requirement> + <requirement type="package" version="3.0">zip</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + structure_name=\$(sed 's/ //g' <<< '$structure.name') && + #if $task.task == 'write': + out_folder=\$(sed 's/.$structure.extension/_displaced/g' <<< '$structure.name') && + ln -s '$structure' \$structure_name && + #if $task.phonon.phonon.phonon_source_type == "castep": + phonon_source_file_name=\$(sed 's/ //g' <<< '$task.phonon.phonon.phonon_source_castep.name') && + ln -s '$task.phonon.phonon.phonon_source_castep' \$phonon_source_file_name && + castep_file_name=\$(sed 's/ //g' <<< '$task.phonon.phonon.castep_file.name') && + ln -s '$task.phonon.phonon.castep_file' \$castep_file_name && + #else if $task.phonon.phonon.phonon_source_type == "dftb+": + phonon_source_file_name=\$(sed 's/ //g' <<< '$task.phonon.phonon.phonon_source_dftb.name') && + ln -s '$task.phonon.phonon.phonon_source_dftb' \$phonon_source_file_name && + gen_file_name=\$(sed 's/ //g' <<< '$task.phonon.phonon.gen_file.name') && + ln -s '$task.phonon.phonon.gen_file' \$gen_file_name && + #end if + #if $task.calculator.script_file: + script_file_name=\$(sed 's/ //g' <<< '$task.calculator.script_file.name') && + ln -s '$task.calculator.script_file' \$script_file_name && + #end if + #if $task.calculator.calculator.calculator == 'castep' and $task.calculator.calculator.castep_param: + castep_param_name=\$(sed 's/ //g' <<< '$task.calculator.calculator.castep_param.name') && + ln -s '$task.calculator.calculator.castep_param' \$castep_param_name && + #end if + ln -s '$params_yaml' params.yaml && + pm-nq -t w \$structure_name params.yaml && + find * > tree.txt && + zip -r out_zip.zip * + #else if $task.task == 'read': + unzip '$task.zipped_input' && + pm-nq -t r \$structure_name params.yaml && + cat averages.dat + #end if + ]]></command> + <configfiles> + <configfile name="params_yaml">#if $task.task == 'write': +method: $task.sampling.method.method +mu_symbol: $task.mu_symbol +mu_index: $task.mu_index +grid_n: $task.sampling.grid_n +sigma_n: $task.sampling.sigma_n +#set $k_points_grid_formatted = $task.calculator.k_points_grid.replace('__ob__', '[').replace('__cb__', ']') +k_points_grid: $k_points_grid_formatted +avgprop: $task.sampling.avgprop +calculator: $task.calculator.calculator.calculator +write_allconf: $task.write_allconf +displace_T: $task.sampling.displace_T +#if $task.sampling.average_T: +average_T: $task.sampling.average_T +#end if +#if $task.sampling.method.method == 'montecarlo' and $task.sampling.method.random_seed: +random_seed: $task.sampling.random_seed +#end if +#if $task.calculator.calculator.calculator == 'dftb+': +dftb_set: $task.calculator.calculator.dftb_set +dftb_pbc: $task.calculator.calculator.dftb_pbc +#end if +phonon_source_type: $task.phonon.phonon.phonon_source_type +#if $task.phonon.phonon.phonon_source_type == 'castep': +#set $phonon_source_file_name = $task.phonon.phonon.phonon_source_castep.name.replace(' ', '') +#else if $task.phonon.phonon.phonon_source_type == 'dftb+': +#set $phonon_source_file_name = $task.phonon.phonon.phonon_source_dftb.name.replace(' ', '') +#end if +phonon_source_file: $phonon_source_file_name +#if $task.calculator.script_file: +#set $script_file_name = $task.calculator.script_file.name.replace(' ', '') +script_file: $script_file_name +#end if +#if $task.calculator.calculator.calculator == 'castep' and $task.calculator.calculator.castep_param: +#set $castep_param_name = $task.calculator.calculator.castep_param.name.replace(' ', '') +castep_param: $castep_param_name +#end if +#end if</configfile> + </configfiles> + <inputs> + <param argument="structure" type="data" format="cell, cif, xyz, extxyz" label="Structure File" help="The muonated structure to make displacements to. The original file will be preserved. Accepted file types: CELL, CIF, XYZ (standard or extended)."/> + <conditional name="task"> + <param argument="task" type="select" display="radio" label="Task" help="Task to perform with pm-nq. Either generate (write) displaced structures, or average (read) those structures."> + <option value="write">Generate</option> + <option value="read">Average</option> + </param> + <when value="write"> + <param argument="mu_symbol" type="text" value="H:mu" label="Muon Symbol" help="Custom label that will be used to identify muon in the structure file."/> + <param argument="mu_index" type="integer" value="-1" label="Muon Index" help="If the Muon Symbol is not present in the cell, then the atom in the cell with this index will be treated as the muon instead. Not used if the Muon Symbol is present. Defaults to the last atom in the structure."/> + <section name="phonon" expanded="true" title="Phonon Source"> + <conditional name="phonon"> + <param argument="phonon_source_type" type="select" display="radio" label="Phonon Type" help="The format of the phonon file."> + <option value="castep">CASTEP</option> + <option value="dftb+">DFTB+</option> + </param> + <when value="castep"> + <param name="phonon_source_castep" type="data" format="txt" label="Phonon File" help="Source file for phonon modes of the muonated structure."/> + <param name="castep_file" type="data" format="castep" label="CASTEP Log (.castep)" help="The CASTEP log produced when generating the Phonon File."/> + </when> + <when value="dftb+"> + <param name="phonon_source_dftb" type="data" format="binary" label="Phonon File" help="Source file for phonon modes of the muonated structure."/> + <param name="gen_file" type="data" format="txt" label="Gen File" help="GEN formatted geometry file for DFTB+."/> + </when> + </conditional> + </section> + <section name="calculator" expanded="true" title="Calculator Settings"> + <conditional name="calculator"> + <param argument="calculator" type="select" display="radio" label="Calculator Type" help="Which software to use to calculate the property."> + <option value="castep">CASTEP</option> + <option value="dftb+">DFTB+</option> + </param> + <when value="castep"> + <param argument="castep_param" type="data" format="txt" optional="true" label="Castep Parameters File" help="For convenience, this file is copied to all output directories (optional)."/> + </when> + <when value="dftb+"> + <expand macro="dftb+"/> + </when> + </conditional> + <expand macro="k_points_grid"/> + <param argument="script_file" type="data" format="txt" optional="true" label="Script File" help="For convenience when running CASTEP or DFTB+, this script file is copied to all output directories. Occurences of {seedname} will be replaced according to the directory name for each job. (optional) "/> + </section> + <section name="sampling" expanded="true" title="Sampling Settings"> + <param argument="avgprop" type="select" display="radio" label="Averaged Property" help="Property to be calculated."> + <option value="hyperfine">Hyperfine</option> + <option value="charge">Charge</option> + </param> + <param argument="displace_T" type="float" value="0" min="0" label="Displacement Temperature" help="Temperature used to generate displacements."/> + <param argument="average_T" type="float" optional="true" min="0" label="Averaging Temperature" help="Temperature used when averaging property (optional). If unset, will use the same value as Displacement Temperature."/> + + <conditional name="method"> + <param argument="method" type="select" display="radio" label="Method" help="Method used to calculate thermal average. Either displaces independently along the three most significant phonon modes (sampling a 3D grid of values) or uses Monte Carlo to randomly sample a fixed number of points from multiple modes at the same time."> + <option value="independent">Independent</option> + <option value="montecarlo">Monte Carlo</option> + </param> + <when value="independent"/> + <when value="montecarlo"> + <param argument="random_seed" type="integer" optional="true" label="Random Seed" help="Seed to use for sampling Monte Carlo distribution."/> + </when> + </conditional> + + <param argument="grid_n" type="integer" value="20" min="1" label="Grid Points" help="Number of points to sample along each phonon mode or thermal line."/> + <param argument="sigma_n" type="float" value="3" min="0" label="Sigma Number" help="Number of sigmas to sample in the harmonic approximation."/> + </section> + <param argument="write_allconf" type="boolean" label="Write All Configurations" help="Whether to write a 'collective' file containing all the displaced positions."/> + </when> + <when value="read"> + <param name="zipped_input" type="data" format="zip" label="Zipped Input" help="A zipped directory structure containing the output of the generate mode, and the results of running CASTEP or DFTB+ to generate the desired property."/> + </when> + </conditional> + <param type="hidden" name="testing" label="Test mode" value="false"/> + </inputs> + <outputs> + <data label="Displaced Structures" name="displaced_structures" format="zip" from_work_dir="out_zip.zip"> + <filter>(task['task'] == 'write')</filter> + </data> + <data label="File tree (testing only)" name="file_tree" format="txt" from_work_dir="tree.txt" hidden="true"> + <filter>(task['task'] == 'write' and testing == 'true')</filter> + </data> + <data label="Averaged Property" name="averaged_property" format="txt" from_work_dir="averages.dat"> + <filter>(task['task'] == 'read')</filter> + </data> + </outputs> + <tests> + <!-- Test CASTEP without default values --> + <test expect_num_outputs="2"> + <param name="testing" value="true"/> + <param name="structure" value="Si.cell" ftype="cell"/> + <conditional name="task"> + <param name="task" value="write"/> + <section name="phonon"> + <conditional name="phonon"> + <param name="phonon_source_castep" value="Si.phonon" ftype="txt"/> + <param name="castep_file" value="Si.castep"/> + </conditional> + </section> + <section name="calculator"> + </section> + <section name="sampling"> + </section> + </conditional> + <output name="file_tree" file="tree.txt" ftype="txt" sort="true"/> + </test> + <!-- Test CASTEP with optional extra files --> + <test expect_num_outputs="2"> + <param name="testing" value="true"/> + <param name="structure" value="Si.cell" ftype="cell"/> + <conditional name="task"> + <param name="task" value="write"/> + <section name="phonon"> + <conditional name="phonon"> + <param name="phonon_source_castep" value="Si.phonon" ftype="txt"/> + <param name="castep_file" value="Si.castep"/> + </conditional> + </section> + <section name="calculator"> + <param name="script_file" value="submit.sh" ftype="txt"/> + <conditional name="calculator"> + <param name="castep_param" value="Si.param"/> + </conditional> + </section> + <section name="sampling"> + </section> + </conditional> + <output name="file_tree" file="tree_extra_files.txt" ftype="txt" sort="true"/> + </test> + <!-- Test DFTB+ --> + <test expect_num_outputs="2"> + <param name="testing" value="true"/> + <param name="structure" value="ethyleneMu_opt.xyz" ftype="xyz"/> + <conditional name="task"> + <param name="task" value="write"/> + <section name="phonon"> + <conditional name="phonon"> + <param name="phonon_source_type" value="dftb+"/> + <param name="phonon_source_dftb" value="ethyleneMu_opt.phonons.pkl" ftype="auto"/> + <param name="gen_file" value="geo_end.gen" ftype="txt"/> + </conditional> + </section> + <section name="calculator"> + <conditional name="calculator"> + <param name="calculator" value="dftb+"/> + </conditional> + </section> + <section name="sampling"> + <conditional name="method"> + <param name="method" value="montecarlo"/> + </conditional> + </section> + </conditional> + <output name="file_tree" file="tree_dftb.txt" ftype="txt" sort="true"/> + </test> + <!-- Test Read Task --> + <test expect_num_outputs="1"> + <param name="structure" value="Si.cell" ftype="cell"/> + <conditional name="task"> + <param name="task" value="read"/> + <param name="zipped_input" value="zipped_input.zip" ftype="zip"/> + </conditional> + <output name="averaged_property" file="averages.dat" ftype="txt"/> + </test> + </tests> + <help><![CDATA[ + Given an input muonated structure (containing a muon), displaces the muon along its normal modes and performs vibrational averaging. There are three steps to using this tool: + 1. Generate displaced structures with `-t w` (write) flag + 2. Calculate the property for all displaced structures using CASTEP or DFTB+ + 3. Average the proprty across all displaced structures with `-t r` (read) flag + + Note that currently only steps 1 and 3 are possible in Galaxy. In order to perform step 2, download the zipped output of step 1, run CASTEP/DFTB+ elsewhere, re-zip the directories including the output properties, and finally run step 3 using this zip file as the input. + + Command-line usage: pm-nq [-h] [-t {r,w}] structure parameter_file + + All data is licensed under the Creative Commons Attribution-ShareAlike 4.0 + International License. The full text of the license can be found at: + + https://creativecommons.org/licenses/by-sa/4.0/legalcode + + For specific data sets remember to cite the following papers, by element : + + | **3-ob-1** + + +--------------+------------------------------------------------+-----------------------------------+------------------------------------+ + | [JCTC2013] | \ J. Chem. Theory Comput., 2013, 9, 338-354. | (O, N, C, H) | https://doi.org/10.1021/ct300849w | + +--------------+------------------------------------------------+-----------------------------------+------------------------------------+ + | [JCTC2014] | \ J. Chem. Theory Comput., 2014, 10, 1518-1537.| (P,S-\*) | https://doi.org/10.1021/ct401002w | + +--------------+------------------------------------------------+-----------------------------------+------------------------------------+ + | [JCTC2015-1] | \ J. Phys. Chem. B, 2015, 119, 1062-1082. | (Mg,Zn-\*) | https://doi.org/10.1021/jp506557r | + +--------------+------------------------------------------------+-----------------------------------+------------------------------------+ + | [JCTC2015-2] | \ J. Chem. Theory Comput., 2015, 11, 332-342. | (Na,F,K,Ca,Cl,Br,I-\*) | https://doi.org/10.1021/ct5009137 | + +--------------+------------------------------------------------+-----------------------------------+------------------------------------+ + + | + | **pbc-0-3** + + +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+ + | [SiC] | \ E. Rauls, R. Gutierrez, J. Elsner, and Th. Frauenheim, Sol. State Comm. 111, 459 (1999) | (Si-C) | https://doi.org/10.1016/S0038-1098(99)00137-4 | + +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+ + | [SiO] | \ C. Koehler, Z. Hajnal, P. Deak, Th. Frauenheim, S. Suhai, Phys. Rev. B 64, 085333 (2001) | (Si-O) | https://doi.org/10.1103/PhysRevB.64.085333 | + +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+ + | [Silicon] | \ A. Sieck, Th. Frauenheim, and K. A. Jackson, phys. stat. sol. (b) 240, 537 (2003). | (Si) | https://doi.org/10.1002/pssb.200301886 | + +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+ + | [Fluorine] | \ C. Koehler and Th. Frauenheim, Surf. Sci. 600, 453 (2006). | \ (F) | https://doi.org/10.1016/j.susc.2005.10.044 | + +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+ + | [Iron] | \ C. Koehler, G. Seifert and Th. Frauenheim, Chem. Phys. 309, 23 (2005). | (Fe) | https://doi.org/10.1016/j.chemphys.2004.03.034 | + +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+ + | [SiSi] | \ A. Sieck, PhD. Thesis, University of Paderborn, 2000. | (Si-Si) | https://www.osti.gov/etdeweb/biblio/20249635 | + +------------+--------------------------------------------------------------------------------------------+---------+------------------------------------------------+ + + | + | The full sets and all other data can be found at the following URLs: + + +----------+------------------------------------------------------------+ + | 3-ob-1 | https://www.dftb.org/parameters/download/3ob/3ob-3-1-cc/ | + +----------+------------------------------------------------------------+ + | pbc-0-3 | https://www.dftb.org/parameters/download/pbc/pbc-0-3-cc/ | + +----------+------------------------------------------------------------+ + + | + .. _Generate muonated structures: /tool_runner?tool_id=pm_muairss_write + ]]></help> + <citations> + <citation type="bibtex"> + @TOOL_CITATION@ + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.castep Fri Feb 03 15:39:49 2023 +0000 @@ -0,0 +1,1115 @@ + +-------------------------------------------------+ + | | + | 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 | + | | + +-------------------------------------------------+ + | | + | Welcome to Academic Release CASTEP version 19.11| + | Ab Initio Total Energy Program | + | | + | Authors: | + | M. Segall, M. Probert, C. Pickard, P. Hasnip, | + | S. Clark, K. Refson, J. R. Yates, M. Payne | + | | + | Contributors: | + | P. Lindan, P. Haynes, J. White, V. Milman, | + | N. Govind, M. Gibson, P. Tulip, V. Cocula, | + | B. Montanari, D. Quigley, M. Glover, | + | L. Bernasconi, A. Perlov, M. Plummer, | + | E. McNellis, J. Meyer, J. Gale, D. Jochym | + | J. Aarons, B. Walker, R. Gillen, D. Jones | + | T. Green, I. J. Bush, C. J. Armstrong, | + | E. J. Higgins, E. L. Brown, M. S. McFly, | + | J. Wilkins, B-C. Shih, P. J. P. Byrne | + | | + | Copyright (c) 2000 - 2018 | + | | + | Distributed under the terms of an | + | Agreement between the United Kingdom | + | Car-Parrinello (UKCP) Consortium, | + | Daresbury Laboratory and Accelrys, Inc. | + | | + | Please cite | + | | + | "First principles methods using CASTEP" | + | | + | Zeitschrift fuer Kristallographie | + | 220(5-6) pp. 567-570 (2005) | + | | + | S. J. Clark, M. D. Segall, C. J. Pickard, | + | P. J. Hasnip, M. J. Probert, K. Refson, | + | M. C. Payne | + | | + | in all publications arising from | + | your use of CASTEP | + | | + +-------------------------------------------------+ + | | + | http://www.castep.org | + | | + +-------------------------------------------------+ + + + + Compiled for linux_x86_64_ifort18 on Wed, 23 Dec 2020 18:08:40 +0000 + from code version + e1fe0d666396+ Castep191_branch Thu, 24 Oct 2019 13:54:03 +0100 + Compiler: Intel Fortran 18.0.3.222; Optimisation: fast + MATHLIBS: Intel MKL(2018.0.3) (LAPACK version 3.7.0) + FFT Lib : default + Fundamental constants values: CODATA 2014 + + Run started: Mon, 31 Oct 2022 16:36:36 +0000 + +-------------------------------------------------+ + | | + | 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 | + | | + +-------------------------------------------------+ + | | + | Welcome to Academic Release CASTEP version 19.11| + | Ab Initio Total Energy Program | + | | + | Authors: | + | M. Segall, M. Probert, C. Pickard, P. Hasnip, | + | S. Clark, K. Refson, J. R. Yates, M. Payne | + | | + | Contributors: | + | P. Lindan, P. Haynes, J. White, V. Milman, | + | N. Govind, M. Gibson, P. Tulip, V. Cocula, | + | B. Montanari, D. Quigley, M. Glover, | + | L. Bernasconi, A. Perlov, M. Plummer, | + | E. McNellis, J. Meyer, J. Gale, D. Jochym | + | J. Aarons, B. Walker, R. Gillen, D. Jones | + | T. Green, I. J. Bush, C. J. Armstrong, | + | E. J. Higgins, E. L. Brown, M. S. McFly, | + | J. Wilkins, B-C. Shih, P. J. P. Byrne | + | | + | Copyright (c) 2000 - 2018 | + | | + | Distributed under the terms of an | + | Agreement between the United Kingdom | + | Car-Parrinello (UKCP) Consortium, | + | Daresbury Laboratory and Accelrys, Inc. | + | | + | Please cite | + | | + | "First principles methods using CASTEP" | + | | + | Zeitschrift fuer Kristallographie | + | 220(5-6) pp. 567-570 (2005) | + | | + | S. J. Clark, M. D. Segall, C. J. Pickard, | + | P. J. Hasnip, M. J. Probert, K. Refson, | + | M. C. Payne | + | | + | in all publications arising from | + | your use of CASTEP | + | | + +-------------------------------------------------+ + | | + | http://www.castep.org | + | | + +-------------------------------------------------+ + + + + Compiled for linux_x86_64_ifort18 on Wed, 23 Dec 2020 18:08:40 +0000 + from code version + e1fe0d666396+ Castep191_branch Thu, 24 Oct 2019 13:54:03 +0100 + Compiler: Intel Fortran 18.0.3.222; Optimisation: fast + MATHLIBS: Intel MKL(2018.0.3) (LAPACK version 3.7.0) + FFT Lib : default + Fundamental constants values: CODATA 2014 + + Run started: Tue, 01 Nov 2022 11:05:44 +0000 + + Warning in parameters_validate: current value of + ELEC_ENERGY_TOL = 0.100000E-07eV + is too large to achieve desired level of convergence of response properties. + This may cause convergence failures and/or inaccuracy of results + of PHONON calculations - recommend you use a smaller value, e.g. + ELEC_ENERGY_TOL ~ 0.100000E-08eV + + Warning in parameters_validate: current value of + ELEC_EIGENVALUE_TOL = 0.400000E-08eV + is too large to achieve desired level of convergence of response properties. + This may cause convergence failures and/or inaccuracy of results + of PHONON calculations - recommend you use a smaller value, e.g. + ELEC_EIGENVALUE_TOL = 0.100000E-08eV + +-------------------------------------------------+ + | | + | D D D D F F F F F P P P P T T T T T | + | D D F P P T | + | D D F F F F P P P P T | + | D D F P T | + | D D D D F P T | + | | + +-------------------------------------------------+ + | | + | Welcome to Castep Linear Response (DFPT) | + | | + | Copyright (c) 2006 - 2018 | + | | + | Please cite the following publications in all | + | work arising from your use of CASTEP LR. | + | | + | K. Refson, S. J. Clark and P. R. Tulip | + | Variational density functional perturbation | + | theory for dielectrics and lattice dynamics | + | Phys. Rev. B 73(15), 155114 (2006) | + +-------------------------------------------------+ + + + Atomic calculation performed for Si: 1s2 2s2 2p6 3s2 3p2 + + Converged in 54 iterations to an ae energy of -7886.857 eV + + ============================================================ + | Pseudopotential Report - Date of generation 1-11-2022 | + ------------------------------------------------------------ + | Element: Si Ionic charge: 4.00 Level of theory: PBE | + | Atomic Solver: Koelling-Harmon | + | | + | Reference Electronic Structure | + | Orbital Occupation Energy | + | 3s 2.000 -0.397 | + | 3p 2.000 -0.150 | + | | + | Pseudopotential Definition | + | Beta l e Rc scheme norm | + | 1 0 -0.397 1.797 qc 0 | + | 2 0 0.250 1.797 qc 0 | + | 3 1 -0.150 1.797 qc 0 | + | 4 1 0.250 1.797 qc 0 | + | 5 2 0.000 1.797 qc 0 | + | 6 2 0.250 1.797 qc 0 | + | loc 3 0.000 1.797 pn 0 | + | | + | Augmentation charge Rinner = 1.255 | + | Partial core correction Rc = 1.255 | + ------------------------------------------------------------ + | "3|1.8|5|6|7|30:31:32" | + ------------------------------------------------------------ + | Author: Chris J. Pickard, Cambridge University | + ============================================================ + + Pseudo atomic calculation performed for Si 3s2 3p2 + + Converged in 20 iterations to a total energy of -165.0690 eV + Calculation parallelised over 8 processes. + Data is distributed by G-vector(8-way) + + ************************************ Title ************************************ + + + ***************************** General Parameters ****************************** + + output verbosity : normal (1) + write checkpoint data to : Si.check + type of calculation : phonon calculation + stress calculation : off + density difference calculation : off + electron localisation func (ELF) calculation : off + Hirshfeld analysis : off + unlimited duration calculation + timing information : on + memory usage estimate : on + write extra output files : on + write final potential to formatted file : off + write final density to formatted file : off + write structure in CELL formatted file : on + write BibTeX reference list : on + write OTFG pseudopotential files : on + write electrostatic potential file : on + write bands file : on + checkpoint writing : write castep_bin only + + output length unit : A + output mass unit : amu + output time unit : ps + output charge unit : e + output spin unit : hbar/2 + output energy unit : eV + output force unit : eV/A + output velocity unit : A/ps + output pressure unit : GPa + output inv_length unit : 1/A + output frequency unit : cm-1 + output force constant unit : eV/A**2 + output volume unit : A**3 + output IR intensity unit : (D/A)**2/amu + output dipole unit : D + output efield unit : eV/A/e + output entropy unit : J/mol/K + + wavefunctions paging : none + random number generator seed : randomised (110544666) + data distribution : optimal for this architecture + optimization strategy : maximize speed(+++) + + *********************** Exchange-Correlation Parameters *********************** + + using functional : Perdew Burke Ernzerhof + relativistic treatment : Koelling-Harmon + DFT+D: Semi-empirical dispersion correction : on + SEDC with : TS correction scheme + + ************************* Pseudopotential Parameters ************************** + + pseudopotential representation : reciprocal space + <beta|phi> representation : reciprocal space + spin-orbit coupling : off + + **************************** Basis Set Parameters ***************************** + + plane wave basis set cut-off : 800.0000 eV + size of standard grid : 1.7500 + size of fine gmax : 25.3584 1/A + finite basis set correction : none + + **************************** Electronic Parameters **************************** + + number of electrons : 32.00 + net charge of system : 0.000 + treating system as non-spin-polarized + number of bands : 20 + + ********************* Electronic Minimization Parameters ********************** + + Method: Treating system as metallic with density mixing treatment of electrons, + and number of SD steps : 1 + and number of CG steps : 4 + + total energy / atom convergence tol. : 0.1000E-07 eV + eigen-energy convergence tolerance : 0.4000E-08 eV + max force / atom convergence tol. : ignored + convergence tolerance window : 3 cycles + max. number of SCF cycles : 200 + number of fixed-spin iterations : 10 + smearing scheme : Gaussian + smearing width : 0.2000 eV + Fermi energy convergence tolerance : 0.2721E-13 eV + periodic dipole correction : NONE + + ************************** Density Mixing Parameters ************************** + + density-mixing scheme : Broyden + max. length of mixing history : 20 + charge density mixing amplitude : 0.8000 + cut-off energy for mixing : 800.0 eV + + *********************** Population Analysis Parameters ************************ + + Population analysis with cutoff : 3.000 A + Population analysis output : summary and pdos components + + ****************************** Phonon Parameters ****************************** + + phonon calculation method : finite displacement + finite displacement amplitude : 0.5292E-02 A + fine phonon calculation method : none + LO/TO splitting term : not included + acoustic phonon sum rule : correct D(q) in recip-space + Born effective charges : not calculated + Raman intensities : not calculated + phonon k-points : use reduced set + phonon DOS : not calculated + backups results every : 3600 seconds + band convergence tolerance : 0.1000E-08 eV + + ******************************************************************************* + + + ------------------------------- + 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 + density = 1.368713 AMU/A**3 + = 2.272802 g/cm^3 + + ------------------------------- + Cell Contents + ------------------------------- + Total number of ions in cell = 8 + Total number of species in cell = 1 + Max number of any one species = 8 + + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx + x Element Atom Fractional coordinates of atoms x + x Number u v w x + x----------------------------------------------------------x + x Si 1 0.000000 0.000000 0.000000 x + x Si 2 0.750000 0.750000 0.250000 x + x Si 3 0.500000 0.000000 0.500000 x + x Si 4 0.750000 0.250000 0.750000 x + x Si 5 0.000000 0.500000 0.500000 x + x Si 6 0.250000 0.250000 0.250000 x + x Si 7 0.250000 0.750000 0.750000 x + x Si 8 0.500000 0.500000 0.000000 x + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx + + + No user defined ionic velocities + + ------------------------------- + Details of Species + ------------------------------- + + Mass of species in AMU + Si 28.0855000 + + Electric Quadrupole Moment (Barn) + Si 1.0000000 No Isotope Defined + + Files used for pseudopotentials: + Si 3|1.8|5|6|7|30:31:32 + + ------------------------------- + k-Points For BZ Sampling + ------------------------------- + MP grid size for SCF calculation is 2 2 2 + with an offset of 0.000 0.000 0.000 + Number of kpoints used = 1 + + ------------------------------- + Symmetry and Constraints + ------------------------------- + + Cell is a supercell containing 4 primitive cells + Maximum deviation from symmetry = 0.993638E-35 ANG + + Number of symmetry operations = 192 + Number of ionic constraints = 24 + Point group of crystal = 32: Oh, m-3m, 4/m -3 2/m + 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 NOT 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 + + -------------------- + DFT-D parameters + -------------------- + + Dispersion-correction scheme : TS + Parameter sR : 0.940000 (default) + Parameter d : 20.000000 (default) + + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx + x Atomic DFT-D parameters x + x Species C6 alpha R0 x + x eV A^6 A^3 A x + x------------------------------------------------------------------x + x Si 182.2457 5.4828 2.2225 (default) x + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx + + ++---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+ +| Memory Disk | +| Baseline code, static data and system overhead 511.0 MB 0.0 MB | +| BLAS internal memory storage 0.0 MB 0.0 MB | +| Model and support data 35.5 MB 0.0 MB | +| Electronic energy minimisation requirements 5.7 MB 0.0 MB | +| Force calculation requirements 2.3 MB 0.0 MB | +| ----------------------------- | +| Approx. total storage required per process 552.2 MB 0.0 MB | +| | +| Requirements will fluctuate during execution and may exceed these estimates | ++-----------------------------------------------------------------------------+ +Calculating total energy with cut-off of 800.000 eV. +------------------------------------------------------------------------ <-- SCF +SCF loop Energy Fermi Energy gain Timer <-- SCF + energy per atom (sec) <-- SCF +------------------------------------------------------------------------ <-- SCF +Initial -7.09593602E+001 0.00000000E+000 6.01 <-- SCF + 1 -1.24858468E+003 7.83639565E+000 1.47203165E+002 6.22 <-- SCF + 2 -1.35797879E+003 4.11673970E+000 1.36742633E+001 6.38 <-- SCF + 3 -1.36375984E+003 4.36603999E+000 7.22630914E-001 6.51 <-- SCF + 4 -1.36326766E+003 4.51593335E+000 -6.15215719E-002 6.74 <-- SCF + 5 -1.36323812E+003 4.61406156E+000 -3.69314988E-003 6.97 <-- SCF + 6 -1.36324494E+003 4.63030923E+000 8.52285266E-004 7.20 <-- SCF + 7 -1.36324642E+003 4.64211529E+000 1.85949274E-004 7.40 <-- SCF + 8 -1.36324644E+003 4.64267854E+000 1.87089627E-006 7.65 <-- SCF + 9 -1.36324644E+003 4.64283116E+000 1.16744203E-007 7.83 <-- SCF + 10 -1.36324644E+003 4.64284504E+000 2.21857767E-009 7.99 <-- SCF + 11 -1.36324644E+003 4.64284138E+000 2.94228120E-010 8.15 <-- SCF +------------------------------------------------------------------------ <-- SCF + +Final energy, E = -1363.246440454 eV +Final free energy (E-TS) = -1363.246440454 eV +(energies not corrected for finite basis set) + +NB est. 0K energy (E-0.5TS) = -1363.246440454 eV + + WARNING: Your unit cell might be too small to get accurate results for van der + Waals +(SEDC) Total Energy Correction : -0.224134E+01 eV + +Dispersion corrected final energy*, Ecor = -1365.487776523 eV +Dispersion corrected final free energy* (Ecor-TS) = -1365.487776523 eV +NB dispersion corrected est. 0K energy* (Ecor-0.5TS) = -1365.487776523 eV + + * not corrected for finite basis set + + +Writing analysis data to Si.castep_bin + ??????????????????????????????????????????????????????????????????????????????? + WARNING: Direct Finite Displacement phonon calculation in primitive cell + (with PHONON_FINE_METHOD = "NONE") at q/=0 is not supported + Calculation A B O R T E D + ??????????????????????????????????????????????????????????????????????????????? + +-------------------------------------------------+ + | | + | 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 | + | | + +-------------------------------------------------+ + | | + | Welcome to Academic Release CASTEP version 19.11| + | Ab Initio Total Energy Program | + | | + | Authors: | + | M. Segall, M. Probert, C. Pickard, P. Hasnip, | + | S. Clark, K. Refson, J. R. Yates, M. Payne | + | | + | Contributors: | + | P. Lindan, P. Haynes, J. White, V. Milman, | + | N. Govind, M. Gibson, P. Tulip, V. Cocula, | + | B. Montanari, D. Quigley, M. Glover, | + | L. Bernasconi, A. Perlov, M. Plummer, | + | E. McNellis, J. Meyer, J. Gale, D. Jochym | + | J. Aarons, B. Walker, R. Gillen, D. Jones | + | T. Green, I. J. Bush, C. J. Armstrong, | + | E. J. Higgins, E. L. Brown, M. S. McFly, | + | J. Wilkins, B-C. Shih, P. J. P. Byrne | + | | + | Copyright (c) 2000 - 2018 | + | | + | Distributed under the terms of an | + | Agreement between the United Kingdom | + | Car-Parrinello (UKCP) Consortium, | + | Daresbury Laboratory and Accelrys, Inc. | + | | + | Please cite | + | | + | "First principles methods using CASTEP" | + | | + | Zeitschrift fuer Kristallographie | + | 220(5-6) pp. 567-570 (2005) | + | | + | S. J. Clark, M. D. Segall, C. J. Pickard, | + | P. J. Hasnip, M. J. Probert, K. Refson, | + | M. C. Payne | + | | + | in all publications arising from | + | your use of CASTEP | + | | + +-------------------------------------------------+ + | | + | http://www.castep.org | + | | + +-------------------------------------------------+ + + + + Compiled for linux_x86_64_ifort18 on Wed, 23 Dec 2020 18:08:40 +0000 + from code version + e1fe0d666396+ Castep191_branch Thu, 24 Oct 2019 13:54:03 +0100 + Compiler: Intel Fortran 18.0.3.222; Optimisation: fast + MATHLIBS: Intel MKL(2018.0.3) (LAPACK version 3.7.0) + FFT Lib : default + Fundamental constants values: CODATA 2014 + + Run started: Tue, 01 Nov 2022 17:23:53 +0000 + + Warning in parameters_validate: current value of + ELEC_ENERGY_TOL = 0.100000E-07eV + is too large to achieve desired level of convergence of response properties. + This may cause convergence failures and/or inaccuracy of results + of PHONON calculations - recommend you use a smaller value, e.g. + ELEC_ENERGY_TOL ~ 0.100000E-08eV + + Warning in parameters_validate: current value of + ELEC_EIGENVALUE_TOL = 0.400000E-08eV + is too large to achieve desired level of convergence of response properties. + This may cause convergence failures and/or inaccuracy of results + of PHONON calculations - recommend you use a smaller value, e.g. + ELEC_EIGENVALUE_TOL = 0.100000E-08eV + +-------------------------------------------------+ + | | + | D D D D F F F F F P P P P T T T T T | + | D D F P P T | + | D D F F F F P P P P T | + | D D F P T | + | D D D D F P T | + | | + +-------------------------------------------------+ + | | + | Welcome to Castep Linear Response (DFPT) | + | | + | Copyright (c) 2006 - 2018 | + | | + | Please cite the following publications in all | + | work arising from your use of CASTEP LR. | + | | + | K. Refson, S. J. Clark and P. R. Tulip | + | Variational density functional perturbation | + | theory for dielectrics and lattice dynamics | + | Phys. Rev. B 73(15), 155114 (2006) | + +-------------------------------------------------+ + +Reading continuation data from model file Si.castep_bin + + Atomic calculation performed for Si: 1s2 2s2 2p6 3s2 3p2 + + Converged in 54 iterations to an ae energy of -7886.857 eV + + ============================================================ + | Pseudopotential Report - Date of generation 1-11-2022 | + ------------------------------------------------------------ + | Element: Si Ionic charge: 4.00 Level of theory: PBE | + | Atomic Solver: Koelling-Harmon | + | | + | Reference Electronic Structure | + | Orbital Occupation Energy | + | 3s 2.000 -0.397 | + | 3p 2.000 -0.150 | + | | + | Pseudopotential Definition | + | Beta l e Rc scheme norm | + | 1 0 -0.397 1.797 qc 0 | + | 2 0 0.250 1.797 qc 0 | + | 3 1 -0.150 1.797 qc 0 | + | 4 1 0.250 1.797 qc 0 | + | 5 2 0.000 1.797 qc 0 | + | 6 2 0.250 1.797 qc 0 | + | loc 3 0.000 1.797 pn 0 | + | | + | Augmentation charge Rinner = 1.255 | + | Partial core correction Rc = 1.255 | + ------------------------------------------------------------ + | "3|1.8|5|6|7|30:31:32" | + ------------------------------------------------------------ + | Author: Chris J. Pickard, Cambridge University | + ============================================================ + + Pseudo atomic calculation performed for Si 3s2 3p2 + + Converged in 20 iterations to a total energy of -165.0690 eV +Initialising basis set for model. +Reinitialising basis set for current geometry. +Continuing from previous run without ground state wavefunction. +Continuing from previous run with ground state density. + Calculation parallelised over 8 processes. + Data is distributed by G-vector(8-way) + + ************************************ Title ************************************ + + + ***************************** General Parameters ****************************** + + output verbosity : normal (1) + continuing from : Si.castep_bin + write checkpoint data to : Si.check + type of calculation : phonon calculation + stress calculation : off + density difference calculation : off + electron localisation func (ELF) calculation : off + Hirshfeld analysis : off + unlimited duration calculation + timing information : on + memory usage estimate : on + write extra output files : on + write final potential to formatted file : off + write final density to formatted file : off + write structure in CELL formatted file : on + write BibTeX reference list : on + write OTFG pseudopotential files : on + write electrostatic potential file : on + write bands file : on + checkpoint writing : write castep_bin only + + output length unit : A + output mass unit : amu + output time unit : ps + output charge unit : e + output spin unit : hbar/2 + output energy unit : eV + output force unit : eV/A + output velocity unit : A/ps + output pressure unit : GPa + output inv_length unit : 1/A + output frequency unit : cm-1 + output force constant unit : eV/A**2 + output volume unit : A**3 + output IR intensity unit : (D/A)**2/amu + output dipole unit : D + output efield unit : eV/A/e + output entropy unit : J/mol/K + + wavefunctions paging : none + random number generator seed : 110544666 + data distribution : optimal for this architecture + optimization strategy : maximize speed(+++) + + *********************** Exchange-Correlation Parameters *********************** + + using functional : Perdew Burke Ernzerhof + relativistic treatment : Koelling-Harmon + DFT+D: Semi-empirical dispersion correction : on + SEDC with : TS correction scheme + + ************************* Pseudopotential Parameters ************************** + + pseudopotential representation : reciprocal space + <beta|phi> representation : reciprocal space + spin-orbit coupling : off + + **************************** Basis Set Parameters ***************************** + + plane wave basis set cut-off : 800.0000 eV + size of standard grid : 1.7500 + size of fine gmax : 25.3584 1/A + finite basis set correction : none + + **************************** Electronic Parameters **************************** + + number of electrons : 32.00 + net charge of system : 0.000 + treating system as non-spin-polarized + number of bands : 20 + + ********************* Electronic Minimization Parameters ********************** + + Method: Treating system as metallic with density mixing treatment of electrons, + and number of SD steps : 1 + and number of CG steps : 4 + + total energy / atom convergence tol. : 0.1000E-07 eV + eigen-energy convergence tolerance : 0.4000E-08 eV + max force / atom convergence tol. : ignored + convergence tolerance window : 3 cycles + max. number of SCF cycles : 200 + number of fixed-spin iterations : 10 + smearing scheme : Gaussian + smearing width : 0.2000 eV + Fermi energy convergence tolerance : 0.2721E-13 eV + periodic dipole correction : NONE + + ************************** Density Mixing Parameters ************************** + + density-mixing scheme : Broyden + max. length of mixing history : 20 + charge density mixing amplitude : 0.8000 + cut-off energy for mixing : 800.0 eV + + *********************** Population Analysis Parameters ************************ + + Population analysis with cutoff : 3.000 A + Population analysis output : summary and pdos components + + ****************************** Phonon Parameters ****************************** + + phonon calculation method : finite displacement + finite displacement amplitude : 0.5292E-02 A + fine phonon calculation method : none + LO/TO splitting term : not included + acoustic phonon sum rule : correct D(q) in recip-space + Born effective charges : not calculated + Raman intensities : not calculated + phonon k-points : use reduced set + phonon DOS : not calculated + backups results every : 3600 seconds + band convergence tolerance : 0.1000E-08 eV + + ******************************************************************************* + + + ------------------------------- + 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 + density = 1.368713 AMU/A**3 + = 2.272802 g/cm^3 + + ------------------------------- + Cell Contents + ------------------------------- + Total number of ions in cell = 8 + Total number of species in cell = 1 + Max number of any one species = 8 + + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx + x Element Atom Fractional coordinates of atoms x + x Number u v w x + x----------------------------------------------------------x + x Si 1 0.000000 0.000000 0.000000 x + x Si 2 0.750000 0.750000 0.250000 x + x Si 3 0.500000 0.000000 0.500000 x + x Si 4 0.750000 0.250000 0.750000 x + x Si 5 0.000000 0.500000 0.500000 x + x Si 6 0.250000 0.250000 0.250000 x + x Si 7 0.250000 0.750000 0.750000 x + x Si 8 0.500000 0.500000 0.000000 x + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx + + + No user defined ionic velocities + + ------------------------------- + Details of Species + ------------------------------- + + Mass of species in AMU + Si 28.0855000 + + Electric Quadrupole Moment (Barn) + Si 1.0000000 No Isotope Defined + + Files used for pseudopotentials: + Si 3|1.8|5|6|7|30:31:32 + + ------------------------------- + k-Points For BZ Sampling + ------------------------------- + MP grid size for SCF calculation is 2 2 2 + with an offset of 0.000 0.000 0.000 + Number of kpoints used = 1 + + ------------------------------- + Symmetry and Constraints + ------------------------------- + + Cell is a supercell containing 4 primitive cells + Maximum deviation from symmetry = 0.993638E-35 ANG + + Number of symmetry operations = 192 + Number of ionic constraints = 24 + Point group of crystal = 32: Oh, m-3m, 4/m -3 2/m + 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 NOT 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 + + -------------------- + DFT-D parameters + -------------------- + + Dispersion-correction scheme : TS + Parameter sR : 0.940000 (default) + Parameter d : 20.000000 (default) + + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx + x Atomic DFT-D parameters x + x Species C6 alpha R0 x + x eV A^6 A^3 A x + x------------------------------------------------------------------x + x Si 182.2457 5.4828 2.2225 (default) x + xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx + + ++---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+ +| Memory Disk | +| Baseline code, static data and system overhead 519.0 MB 0.0 MB | +| BLAS internal memory storage 0.0 MB 0.0 MB | +| Model and support data 35.5 MB 0.0 MB | +| Band structure calculation requirements 1.4 MB 0.0 MB | +| Force calculation requirements 2.3 MB 0.0 MB | +| ----------------------------- | +| Approx. total storage required per process 556.8 MB 0.0 MB | +| | +| Requirements will fluctuate during execution and may exceed these estimates | ++-----------------------------------------------------------------------------+ + Using band-structure calculation to reconstruct wavefunctions from groundstate + density. + ===================================================================== + + + + + B A N D S T R U C T U R E C A L C U L A T I O N + + + + + + Calculation re-parallelised over 8 processes. + + + Data distributed by G-vector(8-way) + + + + + + ================================================================= + + + + + + Band Structure Calculation: Progress report on root process + + + + + + There are 1 BS k-points. Root process contains 1 of them. + + + + + + BS Iteration: 1 of (up to) 60, Time: 0.32s. + + + BS Iteration: 2 of (up to) 60, Time: 0.24s. + + + BS Iteration: 3 of (up to) 60, Time: 0.24s. + + + BS Iteration: 4 of (up to) 60, Time: 0.24s. + + + BS Iteration: 5 of (up to) 60, Time: 0.22s. + + + Spin= 1 of 1, K-point= 1 of 1 completed, Time: 1.39s. + + + Finished BS calculation on root process (waiting for others). + + + + + + ================================================================= + + + Electronic energies + + + ------------------- + + + + + + Band number Energy in eV + + + ================================================================= + + + + + + ----------------------------------------------------------------- + + + Spin=1 kpt= 1 ( -0.250000 -0.250000 -0.250000) kpt-group= 1 + + + ----------------------------------------------------------------- + + + + + + 1 -6.795561 + + + 2 -4.922562 + + + 3 -4.922562 + + + 4 -4.922457 + + + 5 -2.101159 + + + 6 -2.101159 + + + 7 -2.101003 + + + 8 0.332914 + + + 9 0.759541 + + + 10 0.759541 + + + 11 0.759594 + + + 12 2.058762 + + + 13 2.058899 + + + 14 2.058899 + + + 15 3.472965 + + + 16 3.472965 + + + 17 5.755527 + + + 18 5.755527 + + + 19 5.755551 + + + 20 6.157048 + + ===================================================================== + WARNING: Your unit cell might be too small to get accurate results for van der + Waals + Perturbation 1 (of 1): Si 1 X at q=( 0.000, 0.000, 0.000): 6.09s + Parallel strategy changed for perturbation using 2 k-points + Data is distributed by G-vector(4-way) and k-point(2-way) and band(1-way) + +---------------- MEMORY AND SCRATCH DISK ESTIMATES PER PROCESS --------------+ + | Memory Disk | + | Baseline code, static data and system overhead 519.0 MB 0.0 MB | + | BLAS internal memory storage 0.0 MB 0.0 MB | + | Model and support data 35.5 MB 0.0 MB | + | Baseline code, static data and system overhead 519.0 MB 0.0 MB | + | BLAS internal memory storage 0.0 MB 0.0 MB | + | Model and support data 35.5 MB 0.0 MB | + | Finite displacement phonon requirements 12.5 MB 0.0 MB | + | ----------------------------- | + | Approx. total storage required per process 1121.5 MB 0.0 MB | + | | + | Requirements will fluctuate during execution and may exceed these estimates | + +-----------------------------------------------------------------------------+ + + Phonon calculation: q-point 1 (of 1) ( 0.000, 0.000, 0.000): 9.71s + ------------------------------------------------------------------------------- + + ============================================================================== + + Vibrational Frequencies + + + ----------------------- + + + + + + Performing frequency calculation at 1 wavevector (q-pt ) + + + ========================================================================== + + + + + + -------------------------------------------------------------------------- + + + q-pt= 1 ( 0.000000 0.000000 0.000000) 1.0000000000 + + + -------------------------------------------------------------------------- + + + Acoustic sum rule correction < 2.516692 cm-1 applied + + + N Frequency irrep. ir active raman active + + + (cm-1) + + + + + + 1 -0.026685 a N N + + + 2 -0.026685 a N N + + + 3 -0.026685 a N N + + + 4 157.622629 b N N + + + 5 157.622629 b N N + + + 6 157.622629 b N N + + + 7 157.622629 b N N + + + 8 157.622629 b N N + + + 9 157.622629 b N N + + + 10 401.566554 c N N + + + 11 401.566554 c N N + + + 12 401.566554 c N N + + + 13 401.566554 c N N + + + 14 401.566554 c N N + + + 15 401.566554 c N N + + + 16 439.034474 d N N + + + 17 439.034474 d N N + + + 18 439.034474 d N N + + + 19 439.034474 d N N + + + 20 439.034474 d N N + + + 21 439.034474 d N N + + + 22 506.129854 e N Y + + + 23 506.129854 e N Y + + + 24 506.129854 e N Y + + + .......................................................................... + + + Character table from group theory analysis of eigenvectors + + + Point Group = 32, Oh + + + .......................................................................... + + + Rep Mul | E 2' -4 3 m_v m_v I 2" 4 -3 + + + | ---------------------------------------- + + + a T1u 1 | 3 -1 -1 0 1 1 -3 -1 1 0 + + + b ? 1 | 6 -2 0 0 0 0 0 -2 0 0 + + + c ? 1 | 6 2 0 0 2 0 0 0 0 0 + + + d ? 1 | 6 -2 0 0 0 0 0 2 0 0 + + + e T2g 1 | 3 -1 -1 0 1 -1 3 1 -1 0 + + ============================================================================== + + ************** Constrained 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 * + * * + ************************************************************ + + Pseudo atomic calculation performed for Si 3s2 3p2 + + Converged in 20 iterations to a total energy of -165.0690 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 1.363 + Si 5 Px 0.879 + Si 5 Py 0.879 + Si 5 Pz 0.879 + Si 6 S 1.362 + 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 1.363 + 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 + + A BibTeX formatted list of references used in this run has been written to + Si.bib + +Initialisation time = 3.86 s +Calculation time = 6.10 s +Finalisation time = 0.26 s +Total time = 10.21 s +Peak Memory Use = 744044 kB + +Overall parallel efficiency rating: Poor (46%) + +Data was distributed by:- +G-vector (8-way); efficiency rating: Poor (47%) + +Parallel notes: +1) Calculation only took 10.0 s, so efficiency estimates may be inaccurate.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.cell Fri Feb 03 15:39:49 2023 +0000 @@ -0,0 +1,1001 @@ +# CELL file written 11:25:56 (GMT+1.0) 6th September 2021 from run Si + +%BLOCK lattice_cart + ANG + 5.47545112629462 0.496819156878786E-35 0.110608096941637E-35 + 0.496819156878786E-35 5.47545112629462 -0.312695835139248E-35 + 0.110608096941637E-35 -0.312695835139248E-35 5.47545112629462 +%ENDBLOCK lattice_cart + +%BLOCK cell_constraints + 1 1 1 + 0 0 0 +%ENDBLOCK cell_constraints + +%BLOCK positions_frac + Si 0.000000000000000 0.000000000000000 0.000000000000000 + Si 0.750000000000000 0.750000000000000 0.250000000000000 + Si 0.500000000000000 0.000000000000000 0.500000000000000 + Si 0.750000000000000 0.250000000000000 0.750000000000000 + Si 0.000000000000000 0.500000000000000 0.500000000000000 + Si 0.250000000000000 0.250000000000000 0.250000000000000 + Si 0.250000000000000 0.750000000000000 0.750000000000000 + Si 0.500000000000000 0.500000000000000 0.000000000000000 +%ENDBLOCK positions_frac + +FIX_ALL_IONS : true + +%BLOCK species_pot + Si 3|1.8|5|6|7|30:31:32 +%ENDBLOCK species_pot + +SYMMETRY_TOL : 0.001000 + +%BLOCK symmetry_ops +# Symm. op. 1 E + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 2 2 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 3 2 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 4 2 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 5 -4 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 6 -4 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 7 3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 8 3 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 9 3 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 10 3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 11 m + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 12 m + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 13 m + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 14 m + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 15 3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 16 m + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 17 m + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 18 -4 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 19 -4 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 20 -4 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 21 -4 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 22 3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 23 3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 24 3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 0.000000000000000 +# Symm. op. 25 d + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 26 I + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 27 d + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 28 d + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 29 2 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 30 4_1 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 31 4_1 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 32 4_1 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 33 4_1 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 34 -3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 35 -3 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 36 -3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 37 -3 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 38 2_1 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 39 2_1 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 40 4_1 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 41 4_1 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 42 -3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 43 -3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 44 -3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 45 -3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 46 2 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 47 2_1 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 48 2 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.250000000000000 0.250000000000000 0.250000000000000 +# Symm. op. 49 E + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 50 E + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 51 E + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 52 2_1 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 53 2_1 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 54 2 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 55 2 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 56 2_1 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 57 2_1 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 58 2_1 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 59 2 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 60 2_1 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 61 -4 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 62 -4 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 63 3_1 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 64 3_1 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 65 3_1 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 66 3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 67 m + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 68 m + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 69 3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 70 3_1 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 71 m + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 72 m + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 73 -4 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 74 3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 75 3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 76 3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 77 3_1 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 78 m + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 79 m + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 80 n + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 81 -4 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 82 -4 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 83 -4 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 84 -4 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 85 3_1 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 86 3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 87 3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 88 3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 89 m + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 90 -4 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 91 -4 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 92 3_1 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 93 3_1 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 94 3 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 95 3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 96 m + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 97 m + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 98 -4 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 99 -4 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 100 3_1 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 101 3_1 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 102 3 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 103 3_1 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 104 n + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 105 m + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 106 m + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 107 m + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.000000000000000 0.500000000000000 +# Symm. op. 108 n + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 109 m + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 110 3_1 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 111 3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 112 -4 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 113 -4 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 114 -4 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 115 -4 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.500000000000000 0.500000000000000 +# Symm. op. 116 m + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 117 m + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 118 -4 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 119 -4 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 120 -4 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.500000000000000 0.500000000000000 0.000000000000000 +# Symm. op. 121 I + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 122 m? + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 123 m? + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 124 m? + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 125 m? + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 126 I + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 127 m? + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 128 I + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 129 m? + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 130 m? + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 131 m? + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 132 m? + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 133 4_1 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 134 4_2 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 135 -3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 136 -3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 137 -3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 138 -3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 139 2 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 140 2_1 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 141 2_1 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 142 4_2 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 143 4_2 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 144 4_2 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 145 4_1 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 146 -3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 147 -3 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 148 2 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 149 2_1 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 150 4_2 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 151 4_1 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 152 -3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 153 -3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 154 -3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 155 -3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 156 2_1 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 157 2_1 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 158 2_1 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 159 4_2 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 160 4_1 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 161 4_1 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 162 4_2 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 163 -3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 164 -3 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 165 -3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 166 -3 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 167 2_1 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 168 4_1 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 169 4_2 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 170 4_2 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 171 4_2 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 172 -3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 173 -3 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 174 -3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 175 -3 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 176 2_1 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 177 2_1 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 178 4_2 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 179 -3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 180 -3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 181 -3 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 182 -3 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 183 2_1 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 184 2_1 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 185 2 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 186 2_1 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +# Symm. op. 187 2_1 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.750000000000000 0.250000000000000 +# Symm. op. 188 -3 + 0.000000000000000 0.000000000000000 1.000000000000000 + -1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 189 2_1 + 0.000000000000000 1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 190 2_1 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 191 -3 + 0.000000000000000 1.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 -1.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.750000000000000 0.250000000000000 0.750000000000000 +# Symm. op. 192 4_2 + 0.000000000000000 -1.000000000000000 0.000000000000000 + 1.000000000000000 0.000000000000000 0.000000000000000 + 0.000000000000000 0.000000000000000 1.000000000000000 + 0.250000000000000 0.750000000000000 0.750000000000000 +%ENDBLOCK symmetry_ops + +kpoint_mp_grid : 2 2 2 + +%BLOCK PHONON_KPOINT_LIST + 0.0 0.0 0.0 1.0 +%ENDBLOCK PHONON_KPOINT_LIST
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.param Fri Feb 03 15:39:49 2023 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Si.phonon Fri Feb 03 15:39:49 2023 +0000 @@ -0,0 +1,240 @@ + BEGIN header + Number of ions 8 + Number of branches 24 + Number of wavevectors 1 + Frequencies in cm-1 + IR intensities in (D/A)**2/amu + Raman activities in A**4 amu**(-1) + Unit cell vectors (A) + 5.475451 0.000000 0.000000 + 0.000000 5.475451 -0.000000 + 0.000000 -0.000000 5.475451 + Fractional Co-ordinates + 1 0.000000 0.000000 0.000000 Si 28.085500 + 2 0.750000 0.750000 0.250000 Si 28.085500 + 3 0.500000 0.000000 0.500000 Si 28.085500 + 4 0.750000 0.250000 0.750000 Si 28.085500 + 5 0.000000 0.500000 0.500000 Si 28.085500 + 6 0.250000 0.250000 0.250000 Si 28.085500 + 7 0.250000 0.750000 0.750000 Si 28.085500 + 8 0.500000 0.500000 0.000000 Si 28.085500 + END header + q-pt= 1 0.000000 0.000000 0.000000 1.0000000000 + 1 -0.026685 + 2 -0.026685 + 3 -0.026685 + 4 157.622629 + 5 157.622629 + 6 157.622629 + 7 157.622629 + 8 157.622629 + 9 157.622629 + 10 401.566554 + 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0.000000000000 -0.030326167835 0.000000000000 + 22 3 -0.045369375576 0.000000000000 0.349316394268 0.000000000000 0.030326167835 0.000000000000 + 22 4 0.045369375576 0.000000000000 -0.349316394268 0.000000000000 -0.030326167835 0.000000000000 + 22 5 -0.045369375576 0.000000000000 0.349316394268 0.000000000000 0.030326167835 0.000000000000 + 22 6 0.045369375576 0.000000000000 -0.349316394268 0.000000000000 -0.030326167835 0.000000000000 + 22 7 0.045369375576 0.000000000000 -0.349316394268 0.000000000000 -0.030326167835 0.000000000000 + 22 8 -0.045369375576 0.000000000000 0.349316394268 0.000000000000 0.030326167835 0.000000000000 + 23 1 0.195502118074 0.000000000000 0.050586421848 0.000000000000 -0.290206712109 0.000000000000 + 23 2 -0.195502118074 0.000000000000 -0.050586421848 0.000000000000 0.290206712109 0.000000000000 + 23 3 0.195502118074 0.000000000000 0.050586421848 0.000000000000 -0.290206712109 0.000000000000 + 23 4 -0.195502118074 0.000000000000 -0.050586421848 0.000000000000 0.290206712109 0.000000000000 + 23 5 0.195502118074 0.000000000000 0.050586421848 0.000000000000 -0.290206712109 0.000000000000 + 23 6 -0.195502118074 0.000000000000 -0.050586421848 0.000000000000 0.290206712109 0.000000000000 + 23 7 -0.195502118074 0.000000000000 -0.050586421848 0.000000000000 0.290206712109 0.000000000000 + 23 8 0.195502118074 0.000000000000 0.050586421848 0.000000000000 -0.290206712109 0.000000000000 + 24 1 -0.291067932945 0.000000000000 -0.020471214431 0.000000000000 -0.199650664389 0.000000000000 + 24 2 0.291067932945 0.000000000000 0.020471214431 0.000000000000 0.199650664389 0.000000000000 + 24 3 -0.291067932945 0.000000000000 -0.020471214431 0.000000000000 -0.199650664389 0.000000000000 + 24 4 0.291067932945 0.000000000000 0.020471214431 0.000000000000 0.199650664389 0.000000000000 + 24 5 -0.291067932945 0.000000000000 -0.020471214431 0.000000000000 -0.199650664389 0.000000000000 + 24 6 0.291067932945 0.000000000000 0.020471214431 0.000000000000 0.199650664389 0.000000000000 + 24 7 0.291067932945 0.000000000000 0.020471214431 0.000000000000 0.199650664389 0.000000000000 + 24 8 -0.291067932945 0.000000000000 -0.020471214431 0.000000000000 -0.199650664389 0.000000000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/averages.dat Fri Feb 03 15:39:49 2023 +0000 @@ -0,0 +1,208 @@ + +Quantum average of hyperfine tensor calculated on Si.cell. +Scheme details: + +Monte Carlo Normal Displacements Scheme +Displaces all atoms along chosen phonon modes, randomly, +with amplitude determined by the desired temperature. Since they already +follow a normal distribution, all points have equal weight. + +------------------------- + +Modes: +[ 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20] + +Phonon frequencies: +157.62262900000002 157.62262900000002 157.62262900000002 157.62262900000002 157.62262900000002 157.62262900000002 401.5665540000001 401.5665540000001 401.5665540000001 401.5665540000001 401.5665540000001 401.5665540000001 439.03447400000016 439.03447400000016 439.03447400000016 439.03447400000016 439.03447400000016 439.03447400000016 506.1298540000001 506.1298540000001 506.1298540000001 cm^-1 + +Displacement vectors: +[[-0.18229727 -0.32638893 -0.03078031] + [-0.04387154 -0.13106176 0.30297259] + [ 0.17538467 0.32638893 0.06477811] + [ 0.04387154 0.22662018 0.29605998] + [ 0.18229727 -0.27264365 -0.06477811] + [-0.00987374 -0.22662018 -0.30297259] + [ 0.00987374 0.13106176 -0.29605998] + [-0.17538467 0.27264365 0.03078031]] +[[-0.132492 0.28531992 0.00298115] + [ 0.40410302 -0.13733182 0.11692443] + [-0.05332301 -0.28531992 -0.1925135 ] + [-0.40410302 -0.05816283 -0.06889057] + [ 0.132492 -0.33335378 0.1925135 ] + [ 0.21457067 0.05816283 -0.11692443] + [-0.21457067 0.13733182 0.06889057] + [ 0.05332301 0.33335378 -0.00298115]] +[[-0.33097495 0.08266987 -0.00479528] + [-0.00972614 -0.34951037 -0.11572671] + [ 0.23684209 -0.08266987 -0.13599899] + [ 0.00972614 0.21830667 -0.20985956] + [ 0.33097495 0.24291641 0.13599899] + [-0.15052041 -0.21830667 0.11572671] + [ 0.15052041 0.34951037 0.20985956] + [-0.23684209 -0.24291641 0.00479528]] +[[ 2.35321224e-01 -1.29339370e-01 -2.05924437e-02] + [ 1.42989780e-01 -1.42794304e-01 -1.26378822e-01] + [ 1.46536031e-01 1.29339370e-01 -3.94966245e-01] + [-1.42989780e-01 -2.31579497e-01 2.55478433e-01] + [-2.35321224e-01 2.39759077e-04 3.94966245e-01] + [-2.72568909e-01 2.31579497e-01 1.26378822e-01] + [ 2.72568909e-01 1.42794304e-01 -2.55478433e-01] + [-1.46536031e-01 -2.39759077e-04 2.05924437e-02]] +[[ 0.185176 0.19514295 -0.01517808] + [ 0.04914652 0.00698314 -0.33936736] + [ 0.37132414 -0.19514295 0.18493635] + [-0.04914652 0.19313129 0.21713278] + [-0.185176 -0.07290837 -0.18493635] + [ 0.2189048 -0.19313129 0.33936736] + [-0.2189048 -0.00698314 -0.21713278] + [-0.37132414 0.07290837 0.01517808]] +[[-0.0017119 0.02047105 -0.49836359] + [ 0.24863625 0.26714473 -0.00134176] + [-0.03079399 -0.02047105 0.00684378] + [-0.24863625 0.23806264 -0.03384765] + [ 0.0017119 0.01471836 -0.00684378] + [-0.24288356 -0.23806264 0.00134176] + [ 0.24288356 -0.26714473 0.03384765] + [ 0.03079399 -0.01471836 0.49836359]] +[[-0.07146985 -0.20018573 -0.0925623 ] + [ 0.1523907 0.38931326 0.14649988] + [ 0.07146985 -0.20018573 0.0925623 ] + [ 0.1523907 -0.38931326 -0.14649988] + [-0.07146985 0.20018573 0.0925623 ] + [-0.1523907 -0.38931326 0.14649988] + [-0.1523907 0.38931326 -0.14649988] + [ 0.07146985 0.20018573 -0.0925623 ]] +[[-3.46498593e-01 -1.97382238e-01 -2.45913000e-06] + [ 1.97227688e-01 -2.03269327e-01 -1.03739079e-01] + [ 3.46498593e-01 -1.97382238e-01 2.45913000e-06] + [ 1.97227688e-01 2.03269327e-01 1.03739079e-01] + [-3.46498593e-01 1.97382238e-01 2.45913000e-06] + [-1.97227688e-01 2.03269327e-01 -1.03739079e-01] + [-1.97227688e-01 -2.03269327e-01 1.03739079e-01] + [ 3.46498593e-01 1.97382238e-01 -2.45913000e-06]] +[[-0.0055743 -0.23929332 -0.00121731] + [-0.29880574 0.10675833 -0.30335449] + [ 0.0055743 -0.23929332 0.00121731] + [-0.29880574 -0.10675833 0.30335449] + [-0.0055743 0.23929332 0.00121731] + [ 0.29880574 -0.10675833 -0.30335449] + [ 0.29880574 0.10675833 0.30335449] + [ 0.0055743 0.23929332 -0.00121731]] +[[ 0.01343942 0.03803883 -0.49135563] + [-0.02827029 -0.07379457 -0.02640502] + [-0.01343942 0.03803883 0.49135563] + [-0.02827029 0.07379457 0.02640502] + [ 0.01343942 -0.03803883 0.49135563] + [ 0.02827029 0.07379457 -0.02640502] + [ 0.02827029 -0.07379457 0.02640502] + [-0.01343942 -0.03803883 -0.49135563]] +[[-3.52047334e-01 2.21508059e-01 1.00618715e-04] + [-2.36572906e-01 1.03783320e-01 1.01287349e-01] + [ 3.52047334e-01 2.21508059e-01 -1.00618715e-04] + [-2.36572906e-01 -1.03783320e-01 -1.01287349e-01] + [-3.52047334e-01 -2.21508059e-01 -1.00618715e-04] + [ 2.36572906e-01 -1.03783320e-01 1.01287349e-01] + [ 2.36572906e-01 1.03783320e-01 -1.01287349e-01] + [ 3.52047334e-01 -2.21508059e-01 1.00618715e-04]] +[[-0.0261107 0.25137991 -0.00060915] + [ 0.20451772 0.17176383 -0.33881513] + [ 0.0261107 0.25137991 0.00060915] + [ 0.20451772 -0.17176383 0.33881513] + [-0.0261107 -0.25137991 0.00060915] + [-0.20451772 -0.17176383 -0.33881513] + [-0.20451772 0.17176383 0.33881513] + [ 0.0261107 -0.25137991 -0.00060915]] +[[-0.20877514 -0.06073028 -0.00067728] + [-0.08484701 0.40444535 0.05077021] + [ 0.24453015 0.06073028 -0.35626269] + [ 0.08484701 -0.04885994 0.0150152 ] + [ 0.20877514 0.12651568 0.35626269] + [ 0.27209297 0.04885994 -0.05077021] + [-0.27209297 -0.40444535 -0.0150152 ] + [-0.24453015 -0.12651568 0.00067728]] +[[ 0.02582717 -0.21810839 0.01506382] + [ 0.14853047 -0.11164341 -0.17045798] + [-0.3638025 0.21810839 -0.15127903] + [-0.14853047 0.27798626 0.16751735] + [-0.02582717 0.21516776 0.15127903] + [ 0.28474568 -0.27798626 0.17045798] + [-0.28474568 0.11164341 -0.16751735] + [ 0.3638025 -0.21516776 -0.01506382]] +[[-0.00109607 0.03443808 -0.4970452 ] + [-0.2482422 -0.25533597 0.02680904] + [-0.01765348 -0.03443808 -0.00293067] + [ 0.2482422 -0.23877856 0.04555859] + [ 0.00109607 0.03792955 0.00293067] + [ 0.25173367 0.23877856 -0.02680904] + [-0.25173367 0.25533597 -0.04555859] + [ 0.01765348 -0.03792955 0.4970452 ]] +[[-0.06406352 0.38912896 0.05189958] + [-0.0095511 0.00897821 0.27259296] + [-0.07286359 -0.38912896 0.0251431 ] + [ 0.0095511 0.01777827 0.40952008] + [ 0.06406352 0.29298409 -0.0251431 ] + [-0.08659377 -0.01777827 -0.27259296] + [ 0.08659377 -0.00897821 -0.40952008] + [ 0.07286359 -0.29298409 -0.05189958]] +[[ 0.44678146 0.01854844 0.00500064] + [-0.01004145 -0.08702755 0.36326026] + [ 0.14278679 -0.01854844 -0.12493894] + [ 0.01004145 0.21696713 -0.22630799] + [-0.44678146 0.11840384 0.12493894] + [ 0.10989685 -0.21696713 -0.36326026] + [-0.10989685 0.08702755 0.22630799] + [-0.14278679 -0.11840384 -0.00500064]] +[[-4.50209703e-02 -2.13984094e-01 -3.42616356e-04] + [ 3.98652029e-01 -3.32993871e-02 1.06690193e-01] + [ 1.78448684e-01 2.13984094e-01 2.89725812e-01] + [-3.98652029e-01 -2.56769041e-01 -2.67375201e-02] + [ 4.50209703e-02 2.93936768e-01 -2.89725812e-01] + [ 1.09268833e-01 2.56769041e-01 -1.06690193e-01] + [-1.09268833e-01 3.32993871e-02 2.67375201e-02] + [-1.78448684e-01 -2.93936768e-01 3.42616356e-04]] +[[-0.04536938 0.34931639 0.03032617] + [ 0.04536938 -0.34931639 -0.03032617] + [-0.04536938 0.34931639 0.03032617] + [ 0.04536938 -0.34931639 -0.03032617] + [-0.04536938 0.34931639 0.03032617] + [ 0.04536938 -0.34931639 -0.03032617] + [ 0.04536938 -0.34931639 -0.03032617] + [-0.04536938 0.34931639 0.03032617]] +[[ 0.19550212 0.05058642 -0.29020671] + [-0.19550212 -0.05058642 0.29020671] + [ 0.19550212 0.05058642 -0.29020671] + [-0.19550212 -0.05058642 0.29020671] + [ 0.19550212 0.05058642 -0.29020671] + [-0.19550212 -0.05058642 0.29020671] + [-0.19550212 -0.05058642 0.29020671] + [ 0.19550212 0.05058642 -0.29020671]] +[[-0.29106793 -0.02047121 -0.19965066] + [ 0.29106793 0.02047121 0.19965066] + [-0.29106793 -0.02047121 -0.19965066] + [ 0.29106793 0.02047121 0.19965066] + [-0.29106793 -0.02047121 -0.19965066] + [ 0.29106793 0.02047121 0.19965066] + [ 0.29106793 0.02047121 0.19965066] + [-0.29106793 -0.02047121 -0.19965066]] + +Temperature: +0.0 K (displacements), 0.0 K (weights) + +------------------------- + + +Averaged value: + +[[16.9967 -1.0079 1.0534] + [-1.0079 20.9643 0.3008] + [ 1.0534 0.3008 15.061 ]] + +All values, by configuration: + +Conf: 0 (Weight = 1.0) +[[16.9967 -1.0079 1.0534] + [-1.0079 20.9643 0.3008] + [ 1.0534 0.3008 15.061 ]] + + + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ethyleneMu_opt.xyz Fri Feb 03 15:39:49 2023 +0000 @@ -0,0 +1,9 @@ +7 +Properties=species:S:1:pos:R:3:forces:R:3:charge:R:1 energy=-142.22711452331797 pbc="F F F" +C 0.23277597 -0.00000000 0.69727665 0.03325514 0.00000000 0.03920831 -0.15665483 +C -0.07913384 0.00000000 -0.73538585 0.03264532 -0.00000000 0.01286867 -0.28286591 +H -0.15520531 0.88835739 1.20202730 -0.01279691 -0.00215511 -0.00129848 0.07359524 +H -0.15520531 -0.88835739 1.20202730 -0.01279691 0.00215511 -0.00129848 0.07359524 +H -0.08303631 0.92873166 -1.29389186 -0.00112412 0.00267043 0.00211906 0.10320936 +H -0.08303631 -0.92873166 -1.29389186 -0.00112412 -0.00267043 0.00211906 0.10320936 +H 1.32284112 -0.00000000 0.88931832 -0.03805839 -0.00000000 -0.05371812 0.08591154
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/geo_end.gen Fri Feb 03 15:39:49 2023 +0000 @@ -0,0 +1,9 @@ +7 C +C H +1 1 0.232775970233676 0.000000000000440 0.697276654023051 +2 1 -0.079133842353857 -0.000000000000096 -0.735385848255959 +3 2 -0.155205312345435 0.888357392443103 1.202027295837828 +4 2 -0.155205312342459 -0.888357392443973 1.202027295838578 +5 2 -0.083036312707434 0.928731657996102 -1.293891861176065 +6 2 -0.083036312705480 -0.928731657997391 -1.293891861176867 +7 2 1.322841122220987 0.000000000001814 0.899318324909431
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/submit.sh Fri Feb 03 15:39:49 2023 +0000 @@ -0,0 +1,9 @@ +#!/bin/sh +#SBATCH -o %J.o +#SBATCH -e %J.e +#SBATCH -t 24:00:00 +#SBATCH -n 16 +#SBATCH --job-name= {seedname} +#SBATCH --exclusive +module load castep/19 +mpirun castep.mpi {seedname}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tree.txt Fri Feb 03 15:39:49 2023 +0000 @@ -0,0 +1,189 @@ +params.yaml +Si.castep +Si.cell +Si.phonon +Si_displaced +Si_displaced/.collection +Si_displaced/Si_displaced_0 +Si_displaced/Si_displaced_0/Si_displaced_0.cell +Si_displaced/Si_displaced_0/Si_displaced_0.param +Si_displaced/Si_displaced_1 +Si_displaced/Si_displaced_1/Si_displaced_1.cell +Si_displaced/Si_displaced_1/Si_displaced_1.param +Si_displaced/Si_displaced_10 +Si_displaced/Si_displaced_10/Si_displaced_10.cell +Si_displaced/Si_displaced_10/Si_displaced_10.param +Si_displaced/Si_displaced_11 +Si_displaced/Si_displaced_11/Si_displaced_11.cell +Si_displaced/Si_displaced_11/Si_displaced_11.param +Si_displaced/Si_displaced_12 +Si_displaced/Si_displaced_12/Si_displaced_12.cell +Si_displaced/Si_displaced_12/Si_displaced_12.param +Si_displaced/Si_displaced_13 +Si_displaced/Si_displaced_13/Si_displaced_13.cell +Si_displaced/Si_displaced_13/Si_displaced_13.param +Si_displaced/Si_displaced_14 +Si_displaced/Si_displaced_14/Si_displaced_14.cell +Si_displaced/Si_displaced_14/Si_displaced_14.param +Si_displaced/Si_displaced_15 +Si_displaced/Si_displaced_15/Si_displaced_15.cell +Si_displaced/Si_displaced_15/Si_displaced_15.param +Si_displaced/Si_displaced_16 +Si_displaced/Si_displaced_16/Si_displaced_16.cell +Si_displaced/Si_displaced_16/Si_displaced_16.param +Si_displaced/Si_displaced_17 +Si_displaced/Si_displaced_17/Si_displaced_17.cell +Si_displaced/Si_displaced_17/Si_displaced_17.param +Si_displaced/Si_displaced_18 +Si_displaced/Si_displaced_18/Si_displaced_18.cell +Si_displaced/Si_displaced_18/Si_displaced_18.param +Si_displaced/Si_displaced_19 +Si_displaced/Si_displaced_19/Si_displaced_19.cell +Si_displaced/Si_displaced_19/Si_displaced_19.param +Si_displaced/Si_displaced_2 +Si_displaced/Si_displaced_2/Si_displaced_2.cell +Si_displaced/Si_displaced_2/Si_displaced_2.param +Si_displaced/Si_displaced_20 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