Repository 'pm_asephonons'
hg clone https://toolshed.g2.bx.psu.edu/repos/muon-spectroscopy-computational-project/pm_asephonons

Changeset 0:4bc5e66259ca (2022-08-25)
Next changeset 1:641fda3dfb62 (2022-09-15)
Commit message:
planemo upload for repository https://github.com/muon-spectroscopy-computational-project/muon-galaxy-tools/main/pm_asephonons commit d130cf2c46d933fa9d0214ddbd5ddf860f322dc4
added:
pm_asephonons.xml
test-data/Si.cell
test-data/Si.cif
test-data/Si.extxyz
test-data/Si.xyz
test-data/test_out.txt
b
diff -r 000000000000 -r 4bc5e66259ca pm_asephonons.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pm_asephonons.xml Thu Aug 25 16:17:41 2022 +0000
[
b'@@ -0,0 +1,149 @@\n+<tool id="pm_asephonons" name="PyMuonSuite Phonons" version="0.1.1" python_template_version="3.5" profile="22.01">\n+    <description>calculate phonons using ASE and DFTB+</description>\n+    <macros>\n+        <!-- citation should be updated with every underlying tool version -->\n+        <!-- typical fields to update are version, month, year, and doi -->\n+        <token name="@PYMUONSUITE_CITATION@">\n+            @software{pymuon-suite,\n+                author = {Sturniolo, Simone and Liborio, Leandro and Chadwick, Eli and Murgatroyd, Laura and Laverack, Adam and {Muon Spectroscopy Computational Project}},\n+                license = {GPL-3.0},\n+                title = {{pymuon-suite}},\n+                url = {https://github.com/muon-spectroscopy-computational-project/pymuon-suite},\n+                version = {v0.2.1},\n+                month = {2},\n+                year = {2022},\n+                doi = {}\n+            }\n+        </token>\n+    </macros>\n+    <creator>\n+        <person givenName="Jyothish" familyName="Thomas" identifier="https://orcid.org/0000-0003-4724-6924"/>\n+        <person givenName="Eli" familyName="Chadwick" url="https://github.com/elichad" identifier="https://orcid.org/0000-0002-0035-6475"/>\n+        <organization url="https://muon-spectroscopy-computational-project.github.io/index.html" name="The Muon Spectroscopy Computational Project"/>\n+    </creator>\n+    <requirements>\n+        <!-- note versioning is different due to multiple dependencies -->\n+        <requirement type="package" version="0.2.1">pymuonsuite</requirement>\n+        <requirement type="package" version="21.2">dftbplus</requirement>\n+        <requirement type="package" version="1.22.4">numpy</requirement> <!-- pinned due to numpy/ASE/DFTB+ incompatibility https://github.com/dftbplus/dftbplus/issues/1064 -->\n+        <requirement type="package" version="3.0">zip</requirement>\n+    </requirements>\n+    <command detect_errors="exit_code"><![CDATA[\n+        structure_name_internal="input_structure.$structure.ext" &&\n+        touch pho_params.yaml &&\n+        ([[ ! -z "$name" ]] && printf "name: $name \\n">>pho_params.yaml || ( >&2 echo "name empty" && exit 2)) &&\n+        ([[ ! -z "$phonon_kpoint_grid" ]] && ( printf "phonon_kpoint_grid: $phonon_kpoint_grid \\n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>pho_params.yaml || ( >&2 echo "phonon_kpoint_grid empty" && exit 2)) &&\n+        ([[ ! -z "$kpoint_grid" ]] && ( printf "kpoint_grid: $kpoint_grid \\n" | sed "s/__ob__/[/g" | sed "s/__cb__/]/g" )>>pho_params.yaml || ( >&2 echo "kpoint_grid empty" && exit 2)) &&\n+        ([[ ! -z "$force_tol" ]] && printf "force_tol: $force_tol \\n">>pho_params.yaml || ( >&2 echo "force_tol empty" && exit 2)) &&\n+        ([[ ! -z "$dftb_set" ]] && printf "dftb_set: $dftb_set \\n">>pho_params.yaml || ( >&2 echo "dftb_set empty" && exit 2)) &&\n+        ([[ ! -z "$pbc" ]] && printf "pbc: $pbc \\n">>pho_params.yaml || ( >&2 echo "pbc empty" && exit 2)) &&\n+        printf "force_clean: false \\n">>pho_params.yaml &&\n+        ln -s $structure \\$structure_name_internal &&\n+        cat pho_params.yaml &&\n+        pm-asephonons \\$structure_name_internal pho_params.yaml ; err=\\$? &&\n+        echo "Asephonons output:" &&\n+        cat asephonons.out &&\n+        if [ \\$err != 0 ] ; then echo "errored" && exit 24 ; fi &&\n+        ln -s "${name}_phonons.txt" phonon_report.txt &&\n+        zip -r out_zip.zip $name "${name}_phonons.txt" asephonons.out band.out pho_params.yaml\n+    ]]></command>\n+    <inputs>\n+        <param type="data" name="structure" label="Structure file" format="cell" help="The structure to generate the phonon report from. Accepted file types: cell."/>\n+        <param type="text" name="name" label="Structure name" help="Name of the structure." value="struct"/>\n+        <param type="text" name="phonon_kpoint_grid" label="Phonon k-points" value="[1, 1, 1]"/>\n+        <param type="text" name="kpoint_grid" label="K-points used for DFTB+ calculati'..b'B+." value="true"/>\n+    </inputs>\n+    <outputs>\n+        <data label="phonons outputs of $structure.name" name="phonon_outputs" format="zip" from_work_dir="out_zip.zip"/>\n+        <data label="phonon report for $structure.name" name="phonon_report" format="txt" from_work_dir="phonon_report.txt"/>\n+    </outputs>\n+    <tests>\n+        <test>\n+            <param name="structure" value="Si.cell" ftype="cell"/>\n+            <param name="name" value="Si"/>\n+            <param name="dftb_set" value="pbc-0-3"/>\n+            <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">\n+                <assert_contents>\n+                    <has_size value="8155" delta="20"/>\n+                </assert_contents>\n+            </output>\n+        </test>\n+        <test>\n+            <param name="structure" value="Si.cif" ftype="cif"/>\n+            <param name="name" value="Si"/>\n+            <param name="dftb_set" value="pbc-0-3"/>\n+            <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">\n+                <assert_contents>\n+                    <has_size value="8155" delta="20"/>\n+                </assert_contents>\n+            </output>\n+        </test>\n+        <test>\n+            <param name="structure" value="Si.xyz" ftype="xyz"/>\n+            <param name="name" value="Si"/>\n+            <param name="dftb_set" value="pbc-0-3"/>\n+            <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">\n+                <assert_contents>\n+                    <has_size value="8155" delta="20"/>\n+                </assert_contents>\n+            </output>\n+        </test>\n+        <test>\n+            <param name="structure" value="Si.extxyz" ftype="extxyz"/>\n+            <param name="name" value="Si"/>\n+            <param name="dftb_set" value="pbc-0-3"/>\n+            <output name="phonon_report" file="test_out.txt" ftype="txt" compare="re_match">\n+                <assert_contents>\n+                    <has_size value="8155" delta="20"/>\n+                </assert_contents>\n+            </output>\n+        </test>\n+    </tests>\n+    <help><![CDATA[\n+        usage: pm-asephonons structure params\n+\n+        Given an input structure, this tool generates a phonon report for that structure using the parameters provided.\n+\n+    ]]></help>\n+    <citations>\n+        <citation type="bibtex">\n+            @PYMUONSUITE_CITATION@\n+        </citation>\n+        <citation type="bibtex">\n+            @article{doi:10.1063/1.5085197,\n+                author = {Sturniolo,Simone  and Liborio,Leandro  and Jackson,Samuel },\n+                title = {Comparison between density functional theory and density functional tight binding approaches for finding the muon stopping site in organic molecular crystals},\n+                journal = {The Journal of Chemical Physics},\n+                volume = {150},\n+                number = {15},\n+                pages = {154301},\n+                year = {2019},\n+                doi = {10.1063/1.5085197},\n+                URL = {\n+                        https://doi.org/10.1063/1.5085197\n+                },\n+                eprint = {\n+                        https://doi.org/10.1063/1.5085197\n+                }\n+            }\n+        </citation>\n+        <citation type="bibtex">\n+            @article{larsen2017atomic,\n+                title={The atomic simulation environment\xe2\x80\x94a Python library for working with atoms},\n+                author={Larsen, Ask Hjorth and Mortensen, Jens J{\\o}rgen and Blomqvist, Jakob and Castelli, Ivano E and Christensen, Rune and Du{\\l}ak, Marcin and Friis, Jesper and Groves, Michael N and Hammer, Bj{\\o}rk and Hargus, Cory and others},\n+                journal={Journal of Physics: Condensed Matter},\n+                volume={29},\n+                number={27},\n+                pages={273002},\n+                year={2017},\n+                publisher={IOP Publishing}\n+            }\n+        </citation>\n+    </citations>\n+</tool>\n'
b
diff -r 000000000000 -r 4bc5e66259ca test-data/Si.cell
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Si.cell Thu Aug 25 16:17:41 2022 +0000
b
b'@@ -0,0 +1,1000 @@\n+# CELL file written 11:25:56 (GMT+1.0) 6th September 2021 from run Si\n+\n+%BLOCK lattice_cart\n+   ANG\n+       5.47545112629462       0.496819156878786E-35   0.110608096941637E-35\n+      0.496819156878786E-35    5.47545112629462      -0.312695835139248E-35\n+      0.110608096941637E-35  -0.312695835139248E-35    5.47545112629462    \n+%ENDBLOCK lattice_cart\n+\n+%BLOCK cell_constraints\n+      1   1   1\n+      0   0   0\n+%ENDBLOCK cell_constraints\n+\n+%BLOCK positions_frac\n+   Si             0.000000000000000       0.000000000000000       0.000000000000000\n+   Si             0.750000000000000       0.750000000000000       0.250000000000000\n+   Si             0.500000000000000       0.000000000000000       0.500000000000000\n+   Si             0.750000000000000       0.250000000000000       0.750000000000000\n+   Si             0.000000000000000       0.500000000000000       0.500000000000000\n+   Si             0.250000000000000       0.250000000000000       0.250000000000000\n+   Si             0.250000000000000       0.750000000000000       0.750000000000000\n+   Si             0.500000000000000       0.500000000000000       0.000000000000000\n+%ENDBLOCK positions_frac\n+\n+FIX_ALL_IONS : true\n+\n+FIX_COM : true\n+\n+%BLOCK species_pot\n+   Si      3|1.8|5|6|7|30:31:32\n+%ENDBLOCK species_pot\n+\n+SYMMETRY_TOL :     0.001000\n+\n+%BLOCK symmetry_ops\n+# Symm. op. 1       E\n+          1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       1.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000       1.000000000000000\n+          0.000000000000000       0.000000000000000       0.000000000000000\n+# Symm. op. 2       2\n+          1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000      -1.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000      -1.000000000000000\n+          0.000000000000000       0.000000000000000       0.000000000000000\n+# Symm. op. 3       2\n+         -1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000      -1.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000       1.000000000000000\n+          0.000000000000000       0.000000000000000       0.000000000000000\n+# Symm. op. 4       2\n+         -1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       1.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000      -1.000000000000000\n+          0.000000000000000       0.000000000000000       0.000000000000000\n+# Symm. op. 5      -4\n+          0.000000000000000       1.000000000000000       0.000000000000000\n+         -1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000      -1.000000000000000\n+          0.000000000000000       0.000000000000000       0.000000000000000\n+# Symm. op. 6      -4\n+          0.000000000000000       0.000000000000000       1.000000000000000\n+          0.000000000000000      -1.000000000000000       0.000000000000000\n+         -1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000       0.000000000000000\n+# Symm. op. 7       3\n+          0.000000000000000       1.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000       1.000000000000000\n+          1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000       0.000000000000000\n+# Symm. op. 8       3\n+          0.000000000000000       0.000000000000000       1.000000000000000\n+          1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       1.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000       '..b'  0.000000000000000       0.000000000000000      -1.000000000000000\n+          1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       1.000000000000000       0.000000000000000\n+          0.250000000000000       0.750000000000000       0.750000000000000\n+# Symm. op. 182    -3\n+          0.000000000000000      -1.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000       1.000000000000000\n+          1.000000000000000       0.000000000000000       0.000000000000000\n+          0.250000000000000       0.750000000000000       0.750000000000000\n+# Symm. op. 183   2_1\n+          0.000000000000000      -1.000000000000000       0.000000000000000\n+         -1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000      -1.000000000000000\n+          0.250000000000000       0.750000000000000       0.750000000000000\n+# Symm. op. 184   2_1\n+         -1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000       1.000000000000000\n+          0.000000000000000       1.000000000000000       0.000000000000000\n+          0.250000000000000       0.750000000000000       0.750000000000000\n+# Symm. op. 185     2\n+         -1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000      -1.000000000000000\n+          0.000000000000000      -1.000000000000000       0.000000000000000\n+          0.250000000000000       0.750000000000000       0.750000000000000\n+# Symm. op. 186   2_1\n+          0.000000000000000       0.000000000000000      -1.000000000000000\n+          0.000000000000000      -1.000000000000000       0.000000000000000\n+         -1.000000000000000       0.000000000000000       0.000000000000000\n+          0.250000000000000       0.750000000000000       0.750000000000000\n+# Symm. op. 187   2_1\n+          0.000000000000000       0.000000000000000      -1.000000000000000\n+          0.000000000000000      -1.000000000000000       0.000000000000000\n+         -1.000000000000000       0.000000000000000       0.000000000000000\n+          0.750000000000000       0.750000000000000       0.250000000000000\n+# Symm. op. 188    -3\n+          0.000000000000000       0.000000000000000       1.000000000000000\n+         -1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       1.000000000000000       0.000000000000000\n+          0.750000000000000       0.250000000000000       0.750000000000000\n+# Symm. op. 189   2_1\n+          0.000000000000000       1.000000000000000       0.000000000000000\n+          1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000      -1.000000000000000\n+          0.750000000000000       0.250000000000000       0.750000000000000\n+# Symm. op. 190   2_1\n+          0.000000000000000       0.000000000000000       1.000000000000000\n+          0.000000000000000      -1.000000000000000       0.000000000000000\n+          1.000000000000000       0.000000000000000       0.000000000000000\n+          0.750000000000000       0.250000000000000       0.750000000000000\n+# Symm. op. 191    -3\n+          0.000000000000000       1.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000      -1.000000000000000\n+          1.000000000000000       0.000000000000000       0.000000000000000\n+          0.750000000000000       0.250000000000000       0.750000000000000\n+# Symm. op. 192   4_2\n+          0.000000000000000      -1.000000000000000       0.000000000000000\n+          1.000000000000000       0.000000000000000       0.000000000000000\n+          0.000000000000000       0.000000000000000       1.000000000000000\n+          0.250000000000000       0.750000000000000       0.750000000000000\n+%ENDBLOCK symmetry_ops\n+\n+kpoint_mp_grid :    2   2   2\n+\n'
b
diff -r 000000000000 -r 4bc5e66259ca test-data/Si.cif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Si.cif Thu Aug 25 16:17:41 2022 +0000
b
@@ -0,0 +1,33 @@
+data_image0
+_chemical_formula_structural       Si8
+_chemical_formula_sum              "Si8"
+_cell_length_a       5.47545
+_cell_length_b       5.47545
+_cell_length_c       5.47545
+_cell_angle_alpha    90
+_cell_angle_beta     90
+_cell_angle_gamma    90
+
+_space_group_name_H-M_alt    "P 1"
+_space_group_IT_number       1
+
+loop_
+  _space_group_symop_operation_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_type_symbol
+  _atom_site_label
+  _atom_site_symmetry_multiplicity
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_occupancy
+  Si  Si1       1.0  0.00000  0.00000  0.00000  1.0000
+  Si  Si2       1.0  0.75000  0.75000  0.25000  1.0000
+  Si  Si3       1.0  0.50000  0.00000  0.50000  1.0000
+  Si  Si4       1.0  0.75000  0.25000  0.75000  1.0000
+  Si  Si5       1.0  0.00000  0.50000  0.50000  1.0000
+  Si  Si6       1.0  0.25000  0.25000  0.25000  1.0000
+  Si  Si7       1.0  0.25000  0.75000  0.75000  1.0000
+  Si  Si8       1.0  0.50000  0.50000  0.00000  1.0000
b
diff -r 000000000000 -r 4bc5e66259ca test-data/Si.extxyz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Si.extxyz Thu Aug 25 16:17:41 2022 +0000
b
@@ -0,0 +1,10 @@
+8
+Lattice="5.47545112629462 4.96819156878786e-36 1.10608096941637e-36 4.96819156878786e-36 5.47545112629462 -3.12695835139248e-36 1.10608096941637e-36 -3.12695835139248e-36 5.47545112629462" Properties=species:S:1:pos:R:3:initial_magmoms:R:1:castep_labels:S:1 pbc="T T T"
+Si       0.00000000       0.00000000       0.00000000       0.00000000 NULL
+Si       4.10658834       4.10658834       1.36886278       0.00000000 NULL
+Si       2.73772556       0.00000000       2.73772556       0.00000000 NULL
+Si       4.10658834       1.36886278       4.10658834       0.00000000 NULL
+Si       0.00000000       2.73772556       2.73772556       0.00000000 NULL
+Si       1.36886278       1.36886278       1.36886278       0.00000000 NULL
+Si       1.36886278       4.10658834       4.10658834       0.00000000 NULL
+Si       2.73772556       2.73772556      -0.00000000       0.00000000 NULL
b
diff -r 000000000000 -r 4bc5e66259ca test-data/Si.xyz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Si.xyz Thu Aug 25 16:17:41 2022 +0000
b
@@ -0,0 +1,10 @@
+8
+Generated by cif2cell 2.0.0.  :  Kitano, A. et al., Physical Review, Serie 3. B - Condensed Matter (18,1978-) 64, 0452061-0452069 (2001).
+Si    0.000000000000000   0.000000000000000   0.000000000000000
+Si    4.035750000000000   4.035750000000000   1.345250000000000
+Si    2.690500000000000   0.000000000000000   2.690500000000000
+Si    4.035750000000000   1.345250000000000   4.035750000000000
+Si    0.000000000000000   2.690500000000000   2.690500000000000
+Si    1.345250000000000   1.345250000000000   1.345250000000000
+Si    1.345250000000000   4.035750000000000   4.035750000000000
+Si    2.690500000000000   2.690500000000000   0.000000000000000
b
diff -r 000000000000 -r 4bc5e66259ca test-data/test_out.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_out.txt Thu Aug 25 16:17:41 2022 +0000
[
@@ -0,0 +1,290 @@
+
+    \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*
+    \|                          \|
+    \|       PYMUON-SUITE       \|
+    \|    ASE Phonons report    \|
+    \|                          \|
+    \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*
+
+    Name: Si
+    Date: \d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}.\d{6}
+    Structure file: input_structure.(cell|cif|xyz|extxyz)
+    Parameter file: pho_params.yaml
+
+    \*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*\*
+
+    K-point Path:
+ \[0. 0. 0.\]
+
+
+------------------
+
+K-point 1: \[0. 0. 0.\]
+
+ Frequencies \(cm\^-1\):
+ 1\t-?\d+\.\d+(e[+-]?\d+)?
+ 2\t-?\d+\.\d+(e[+-]?\d+)?
+ 3\t-?\d+\.\d+(e[+-]?\d+)?
+ 4\t-?\d+\.\d+(e[+-]?\d+)?
+ 5\t-?\d+\.\d+(e[+-]?\d+)?
+ 6\t-?\d+\.\d+(e[+-]?\d+)?
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+ 23\t-?\d+\.\d+(e[+-]?\d+)?
+ 24\t-?\d+\.\d+(e[+-]?\d+)?
+
+ Displacements:
+ Mode 1:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
+ 5(\t[- ]\d+\.\d+){3}
+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 2:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
+ 5(\t[- ]\d+\.\d+){3}
+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 3:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 4:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 5:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 6:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 7:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
+ 5(\t[- ]\d+\.\d+){3}
+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 8:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 9:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 10:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 11:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
+ 5(\t[- ]\d+\.\d+){3}
+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 12:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
+ 5(\t[- ]\d+\.\d+){3}
+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 13:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
+ 5(\t[- ]\d+\.\d+){3}
+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 14:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
+ 5(\t[- ]\d+\.\d+){3}
+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 15:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 16:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 17:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 18:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
+ 5(\t[- ]\d+\.\d+){3}
+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 19:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 20:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 21:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
+ 5(\t[- ]\d+\.\d+){3}
+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 22:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
+ 5(\t[- ]\d+\.\d+){3}
+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 23:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
+ Mode 24:
+ Atom x  y  z
+ 1(\t[- ]\d+\.\d+){3}
+ 2(\t[- ]\d+\.\d+){3}
+ 3(\t[- ]\d+\.\d+){3}
+ 4(\t[- ]\d+\.\d+){3}
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+ 6(\t[- ]\d+\.\d+){3}
+ 7(\t[- ]\d+\.\d+){3}
+ 8(\t[- ]\d+\.\d+){3}
\ No newline at end of file