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planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_dftb_opt commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
author muon-spectroscopy-computational-project
date Thu, 25 Aug 2022 16:18:08 +0000
parents
children 23cb25b1d776
files README-3ob README-pbc get_out_folder.py pm_dftb_opt.xml run.sh test-data/muonated-dftb.zip test-data/tree.txt
diffstat 7 files changed, 504 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README-3ob	Thu Aug 25 16:18:08 2022 +0000
@@ -0,0 +1,115 @@
+======================================================================
+3ob-3-1
+======================================================================
+
+(c) 2017, Marcus Elstner, Karlsruher Institut für Technologie
+All rights reserved
+
+This work is licensed under the Creative Commons Attribution-ShareAlike 4.0
+International License. To view a copy of this license, consult the LICENSE file
+or visit http://creativecommons.org/licenses/by-sa/4.0/ .
+
+NOTE: The rights holder(s) for this work explicitly require that the attribution
+conditions of this license are enforced. Use in part or in whole of this data is
+permitted only under the condition that the scientific background of the
+Licensed Material will be CITED IN ANY PUBLICATIONS ARISING FROM ITS USE. The
+required references are specified in this file and must be included in resulting works.
+
+
+Description
+===========
+
+This set of parameters is part of the Third-Order Parametrization for
+Organic and Biological Systems (3OB) has been specifically designed
+for Third Order Density Functional Tight Binding (DFTB3) and super-
+sedes the MIO parameter set. Main improvements over MIO are improved
+geometries for non-covalent bonds as e.g. the hydrogen bond in the
+water dimer, a great reduction of the consistent overbinding and an
+overall improved performance. Comprehensive benchmark tests for
+C-H-N-O can be found in [JCTC2013], for P-S-* in [JCTC2014],
+for Mg-Zn-* in [JCTC2015-1], and for Na-F-K-Ca-Cl-Br-I-* in
+[JCTC2015-2].
+
+----------------------------------------------------------------------
+
+The following parameter should be generally used for DFTB3/3OB
+calculations:
+
+zeta = 4.00 (gamma^h function exponent; DampXHExponent in DFTB+)
+
+----------------------------------------------------------------------
+
+List of all atomic Hubbard derivatives (atomic units):
+Br = -0.0573
+ C = -0.1492
+Ca = -0.0340
+Cl = -0.0697
+ F = -0.1623
+ H = -0.1857
+ I = -0.0433
+ K = -0.0339
+Mg = -0.02
+ N = -0.1535
+Na = -0.0454
+ O = -0.1575
+ P = -0.14
+ S = -0.11
+Zn = -0.03
+
+Maximum angular momenta for calculation input files:
+
+Br = "d"
+ C = "p"
+Ca = "p"
+Cl = "d"
+ F = "p"
+ H = "s"
+ I = "d"
+ K = "p"
+Mg = "p"
+ N = "p"
+Na = "p"
+ O = "p"
+ P = "d"
+ S = "d"
+Zn = "d"
+
+----------------------------------------------------------------------
+
+For the empirical halogend bond correction described in [JCTC2015-2]
+the following parameters are provided:
+
+DFTB3-D3(BJ) Parameters:
+a1 = 0.746
+a2 = 4.191
+s8 = 3.209
+
+General X-Correction parameters (AA and kcal/mol unit system):
+c1 = 7.761
+c2 = 0.050
+c3 = 4.518
+
+Element Pair Parameters (AA and kcal/mol unit system):
+O-Cl = 1.237
+O-Br = 1.099
+O-I  = 1.313
+N-Cl = 1.526
+N-Br = 1.349
+N-I  = 1.521
+
+
+Relevant Publications
+=====================
+
+[JCTC2013] J. Chem. Theory Comput., 2013, 9, 338-354.
+[JCTC2014] J. Chem. Theory Comput., 2014, 10, 1518–1537.
+[JCTC2015-1] J. Phys. Chem. B, 2015, 119, 1062–1082.
+[JCTC2015-2] J. Chem. Theory Comput., 2015, 11, 332–342.
+
+
+Required references
+===================
+O - N - C - H:		[JCTC2013]
+P,S-*:	    		[JCTC2014]
+Mg,Zn-*:		[JCTC2015-1]
+Na,F,K,Ca,Cl,Br,I-*:	[JCTC2015-2]
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README-pbc	Thu Aug 25 16:18:08 2022 +0000
@@ -0,0 +1,65 @@
+(c) 2017, Thomas Frauenheim, Universität Bremen
+All rights reserved
+
+This work is licensed under the Creative Commons Attribution-ShareAlike 4.0
+International License. To view a copy of this license, consult the LICENSE file
+or visit http://creativecommons.org/licenses/by-sa/4.0/ .
+
+NOTE: The rights holder(s) for this work explicitly require that the attribution
+conditions of this license are enforced. Use in part or in whole of this data is
+permitted only under the condition that the scientific background of the
+Licensed Material will be CITED IN ANY PUBLICATIONS ARISING FROM ITS USE. The
+required references are specified in this file and must be included in resulting works.
+
+
+Description
+-----------
+
+This set consists of mainly older Slater-Koster files with a focus on
+solid state systems [SiO,SiC]. The parameters might also
+be applicable for organic systems, but one usually would only expect a
+more qualitative accuracy. So use the "bio" set instead for bio molecules.
+
+The silicon parameters are good for silicon clusters (using a sp basis
+only) [Silicon], while the same parameters with d-orbitals on Si are
+used for silica.
+
+The fluorine parameters have been validated especially
+concerning the relative energetics of SiF_x and CF_x [Fluorine].
+
+The iron parameters have been applied to structural and magnetic
+properties of iron clusters [Iron], but should also give reasonable
+results for bcc bulk iron.
+
+Relevant Publications
+---------------------
+To many to give here one by one. In summary:
+
+- all publications since 1999 of the Frauenheim group dealing with SiC bulk, 
+  especially: Rauls, E. and Gutierrez, R. and Elsner, J. and Frauenheim, Th.,
+  Stoichiometric and Non-Stoichiometric (10-10) and (11-20) surfaces in 
+  {2H-SiC}: a theoretical study, Sol. State Comm., p. 459, vol. 111
+  (1999)
+- [SiO]: all publications of the Frauenheim group dealing with SiO polymorphs,
+  especially Koehler, C. and Hajnal, Z. and Deak, P. and Frauenheim,
+  Th. and Suhai, S.. Theoretical investigation of carbon defects and
+  diffusion in alpha-quartz. Phys. Rev. B, 64:085333, 2001.
+- [Silicon]: A. Sieck and Th. Frauenheim and K. A. Jackson
+  phys. stat. sol. (b), p. 537, year 2003, vol. 240
+- [Fluorine]: Koehler, C. and Frauenheim, T.. Molecular dynamics simulations of
+  CFx (x=2,3) molecules at Si3N4 and SiO2 surfaces. Surf. Sci., 600:453,
+  2006.
+- [Iron]: Koehler, C. and Seifert, G. and Frauenheim, T..
+  Density-Functional based calculations for Fe(n), (n<=32). Chem.
+  Phys., 309:23, 2005.
+
+Required references
+-------------------
+Si-Si: 	A. Sieck, PhD. Thesis, University of Paderborn, 2000.
+       	http://ubdata.uni-paderborn.de/ediss/06/2000/sieck/
+Si-O:   [SiO]
+F-*: 	[Fluorine]
+Fe-Fe:	[Iron]
+
+* stands for all available elements in this set
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_out_folder.py	Thu Aug 25 16:18:08 2022 +0000
@@ -0,0 +1,11 @@
+import sys
+
+import yaml
+
+
+try:
+    with open('params.yaml') as f:
+        data = yaml.safe_load(f)
+    sys.stdout.write(data['out_folder'])
+except KeyError:
+    sys.stdout.write('muon-airss-out')
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pm_dftb_opt.xml	Thu Aug 25 16:18:08 2022 +0000
@@ -0,0 +1,142 @@
+<tool id="pm_dftb_opt" name="PyMuonSuite AIRSS DFTB+ Optimise" version="0.1.1" python_template_version="3.5" profile="22.01">
+    <description>run DFTB+ optimisation</description>
+    <macros>
+        <!-- citation should be updated with every underlying tool version -->
+        <!-- typical fields to update are version, month, year, and doi -->
+        <token name="@PYMUONSUITE_CITATION@">
+            @software{pymuon-suite,
+                author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}},
+                license = {GPL-3.0},
+                title = {{pymuon-suite}},
+                url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},
+                version = {v0.2.1},
+                month = {2},
+                year = {2022},
+                doi = {}
+            }
+        </token>
+    </macros>
+    <creator>
+        <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>
+        <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>
+        <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>
+    </creator>
+    <requirements>
+        <!-- note versioning is different due to multiple dependencies -->
+        <requirement type="package" version="21.2">dftbplus</requirement>
+        <requirement type="package" version="0.2.1">pymuonsuite</requirement>
+        <requirement type="package" version="3.0">zip</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        unzip "$muonated_structures" &&
+        if test -f "params.yaml"; then echo "params.yaml present"; else echo "params.yaml missing" && exit 64; fi
+        && if ( test -f input_structure.* ) ; then echo "input structure present"; else echo "input structure missing" && exit 64; fi
+        && out_folder="`python ${__tool_directory__}/get_out_folder.py`" ;
+        bash ${__tool_directory__}/run.sh \$out_folder ;
+        passed=$? &&
+        echo \$passed &&
+        if [ \$passed == 2 ]; then echo "input file structure is not dftb" && exit 25; elif [ \$passed == 3 ]; then echo "error in parsing dftb file. check log for details" && exit 26; else echo "parse ok"; fi &&
+        if grep -q 'pbc-0-3' params.yaml; then cp ${__tool_directory__}/README-pbc \$out_folder/README; elif grep -q '3ob-3-1' params.yaml; then cp ${__tool_directory__}/README-3ob \$out_folder README; else ( cp ${__tool_directory__}/README-3ob \$out_folder README-3ob && cp ${__tool_directory__}/README-pbc \$out_folder/README-pbc ); fi;
+        zip -r dftb_results.zip \$out_folder params.yaml input_structure.* &&
+        find \$out_folder > tree.txt
+    ]]></command>
+    <inputs>
+        <param type="data" name="muonated_structures" label="Muonated structures (.zip)" format="zip" help="A zip folder containing muonated structures, as generated by the 'Generate muonated structures' tool or pm-muairss."/>
+        <param type="hidden" name="testing" label="Test mode" value="false"/>
+    </inputs>
+    <outputs>
+        <data label="DFTB results for $muonated_structures.name" name="dftb_results" format="zip" from_work_dir="dftb_results.zip"/>
+        <data label="File tree (testing only)" name="file_tree" format="txt" from_work_dir="tree.txt" hidden="true">
+            <filter>(testing == "true")</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="testing" value="true"/>
+            <param name="muonated_structures" value="muonated-dftb.zip" ftype="zip"/>
+            <output name="file_tree" file="tree.txt" ftype="txt" sort="true"/>
+        </test>
+        <!-- check that file_tree filter works -->
+        <test expect_num_outputs="1">
+            <param name="testing" value="false"/>
+            <param name="muonated_structures" value="muonated-dftb.zip" ftype="zip"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        usage: dftb+
+        Given some input muonated structures (structures containing a muon), applies DFTB+ optimization to refine them.
+
+        **LICENSE**
+
+        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/  |
++----------+------------------------------------------------------------+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @PYMUONSUITE_CITATION@
+        </citation>
+        <citation type="bibtex">
+        @article{doi:10.1063/1.5143190,
+         author = {Hourahine,B.  and Aradi,B.  and Blum,V.  and Bonafé,F.  and Buccheri,A.  and Camacho,C.  and Cevallos,C.  and Deshaye,M. Y.  and Dumitrică,T.  and Dominguez,A.  and Ehlert,S.  and Elstner,M.  and van der Heide,T.  and Hermann,J.  and Irle,S.  and Kranz,J. J.  and Köhler,C.  and Kowalczyk,T.  and Kubař,T.  and Lee,I. S.  and Lutsker,V.  and Maurer,R. J.  and Min,S. K.  and Mitchell,I.  and Negre,C.  and Niehaus,T. A.  and Niklasson,A. M. N.  and Page,A. J.  and Pecchia,A.  and Penazzi,G.  and Persson,M. P.  and Řezáč,J.  and Sánchez,C. G.  and Sternberg,M.  and Stöhr,M.  and Stuckenberg,F.  and Tkatchenko,A.  and Yu,V. W.-z.  and Frauenheim,T. },
+         title = {DFTB+, a software package for efficient approximate density functional theory based atomistic simulations},
+         journal = {The Journal of Chemical Physics},
+         volume = {152},
+         number = {12},
+         pages = {124101},
+         year = {2020},
+         doi = {10.1063/1.5143190},
+
+         URL = {
+                 https://doi.org/10.1063/1.5143190
+
+         },
+         eprint = {
+                 https://doi.org/10.1063/1.5143190
+         }
+         }
+        </citation>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run.sh	Thu Aug 25 16:18:08 2022 +0000
@@ -0,0 +1,14 @@
+#! /bin/bash
+
+set -o errexit
+[ ! -d "$1/dftb+" ] && ( echo 1>&2 "no dftb+ structures found" && exit 2 )
+for x in $1/dftb+/* 
+do 
+    
+    if ! out=$(echo $x && cd $x && dftb+)
+    then 
+    echo 1>&2 "$out"; exit 3
+    else
+    echo "$out"
+    fi
+done || exit 
\ No newline at end of file
Binary file test-data/muonated-dftb.zip has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/tree.txt	Thu Aug 25 16:18:08 2022 +0000
@@ -0,0 +1,157 @@
+Si-out
+Si-out/dftb.LICENSE
+Si-out/dftb+
+Si-out/dftb+/Si_1
+Si-out/dftb+/Si_1/dftb_in.hsd
+Si-out/dftb+/Si_1/geo_end.gen
+Si-out/dftb+/Si_1/dftb_pin.hsd
+Si-out/dftb+/Si_1/results.tag
+Si-out/dftb+/Si_1/band.out
+Si-out/dftb+/Si_1/detailed.out
+Si-out/dftb+/Si_1/geo_end.xyz
+Si-out/dftb+/Si_2
+Si-out/dftb+/Si_2/dftb_in.hsd
+Si-out/dftb+/Si_2/geo_end.gen
+Si-out/dftb+/Si_2/dftb_pin.hsd
+Si-out/dftb+/Si_2/results.tag
+Si-out/dftb+/Si_2/band.out
+Si-out/dftb+/Si_2/detailed.out
+Si-out/dftb+/Si_2/geo_end.xyz
+Si-out/dftb+/Si_3
+Si-out/dftb+/Si_3/dftb_in.hsd
+Si-out/dftb+/Si_3/geo_end.gen
+Si-out/dftb+/Si_3/dftb_pin.hsd
+Si-out/dftb+/Si_3/results.tag
+Si-out/dftb+/Si_3/band.out
+Si-out/dftb+/Si_3/detailed.out
+Si-out/dftb+/Si_3/geo_end.xyz
+Si-out/dftb+/Si_4
+Si-out/dftb+/Si_4/dftb_in.hsd
+Si-out/dftb+/Si_4/geo_end.gen
+Si-out/dftb+/Si_4/dftb_pin.hsd
+Si-out/dftb+/Si_4/results.tag
+Si-out/dftb+/Si_4/band.out
+Si-out/dftb+/Si_4/detailed.out
+Si-out/dftb+/Si_4/geo_end.xyz
+Si-out/dftb+/Si_5
+Si-out/dftb+/Si_5/dftb_in.hsd
+Si-out/dftb+/Si_5/geo_end.gen
+Si-out/dftb+/Si_5/dftb_pin.hsd
+Si-out/dftb+/Si_5/results.tag
+Si-out/dftb+/Si_5/band.out
+Si-out/dftb+/Si_5/detailed.out
+Si-out/dftb+/Si_5/geo_end.xyz
+Si-out/dftb+/Si_6
+Si-out/dftb+/Si_6/dftb_in.hsd
+Si-out/dftb+/Si_6/geo_end.gen
+Si-out/dftb+/Si_6/dftb_pin.hsd
+Si-out/dftb+/Si_6/results.tag
+Si-out/dftb+/Si_6/band.out
+Si-out/dftb+/Si_6/detailed.out
+Si-out/dftb+/Si_6/geo_end.xyz
+Si-out/dftb+/Si_7
+Si-out/dftb+/Si_7/dftb_in.hsd
+Si-out/dftb+/Si_7/geo_end.gen
+Si-out/dftb+/Si_7/dftb_pin.hsd
+Si-out/dftb+/Si_7/results.tag
+Si-out/dftb+/Si_7/band.out
+Si-out/dftb+/Si_7/detailed.out
+Si-out/dftb+/Si_7/geo_end.xyz
+Si-out/dftb+/Si_8
+Si-out/dftb+/Si_8/dftb_in.hsd
+Si-out/dftb+/Si_8/geo_end.gen
+Si-out/dftb+/Si_8/dftb_pin.hsd
+Si-out/dftb+/Si_8/results.tag
+Si-out/dftb+/Si_8/band.out
+Si-out/dftb+/Si_8/detailed.out
+Si-out/dftb+/Si_8/geo_end.xyz
+Si-out/dftb+/Si_9
+Si-out/dftb+/Si_9/dftb_in.hsd
+Si-out/dftb+/Si_9/geo_end.gen
+Si-out/dftb+/Si_9/dftb_pin.hsd
+Si-out/dftb+/Si_9/results.tag
+Si-out/dftb+/Si_9/band.out
+Si-out/dftb+/Si_9/detailed.out
+Si-out/dftb+/Si_9/geo_end.xyz
+Si-out/dftb+/Si_10
+Si-out/dftb+/Si_10/dftb_in.hsd
+Si-out/dftb+/Si_10/geo_end.gen
+Si-out/dftb+/Si_10/dftb_pin.hsd
+Si-out/dftb+/Si_10/results.tag
+Si-out/dftb+/Si_10/band.out
+Si-out/dftb+/Si_10/detailed.out
+Si-out/dftb+/Si_10/geo_end.xyz
+Si-out/dftb+/Si_11
+Si-out/dftb+/Si_11/dftb_in.hsd
+Si-out/dftb+/Si_11/geo_end.gen
+Si-out/dftb+/Si_11/dftb_pin.hsd
+Si-out/dftb+/Si_11/results.tag
+Si-out/dftb+/Si_11/band.out
+Si-out/dftb+/Si_11/detailed.out
+Si-out/dftb+/Si_11/geo_end.xyz
+Si-out/dftb+/Si_12
+Si-out/dftb+/Si_12/dftb_in.hsd
+Si-out/dftb+/Si_12/geo_end.gen
+Si-out/dftb+/Si_12/dftb_pin.hsd
+Si-out/dftb+/Si_12/results.tag
+Si-out/dftb+/Si_12/band.out
+Si-out/dftb+/Si_12/detailed.out
+Si-out/dftb+/Si_12/geo_end.xyz
+Si-out/dftb+/Si_13
+Si-out/dftb+/Si_13/dftb_in.hsd
+Si-out/dftb+/Si_13/geo_end.gen
+Si-out/dftb+/Si_13/dftb_pin.hsd
+Si-out/dftb+/Si_13/results.tag
+Si-out/dftb+/Si_13/band.out
+Si-out/dftb+/Si_13/detailed.out
+Si-out/dftb+/Si_13/geo_end.xyz
+Si-out/dftb+/Si_14
+Si-out/dftb+/Si_14/dftb_in.hsd
+Si-out/dftb+/Si_14/geo_end.gen
+Si-out/dftb+/Si_14/dftb_pin.hsd
+Si-out/dftb+/Si_14/results.tag
+Si-out/dftb+/Si_14/band.out
+Si-out/dftb+/Si_14/detailed.out
+Si-out/dftb+/Si_14/geo_end.xyz
+Si-out/dftb+/.collection
+Si-out/pbc-0-3
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+Si-out/pbc-0-3/C-F.skf
+Si-out/pbc-0-3/C-H.skf
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+Si-out/pbc-0-3/Si-O.skf
+Si-out/pbc-0-3/Si-Si.skf
+Si-out/README