mirror of https://github.com/phonopy/phonopy.git
cp2k: implement full cell spec parsing
* previously we only allowed for orthorombic cells, with the help of the new cp2k-input-tools we can now parse any cell spec * switching to cp2k-input-tools allows to parse almost any CP2K input * switch to using Angstrom (CP2K's default for distances)
This commit is contained in:
Tiziano Müller
parent
c14d77d032
commit
88c3b12129
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@ -1,20 +0,0 @@
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This is an example of CP2K interface.
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To create supercells with displacements:
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% phonopy --cp2k -c Si.inp -d --dim="2 2 2"
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A perfect 2x2x2 supercell (supercell.in) and one 2x2x2 supercells
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(supercell-xxx.in) of the conventional unit cell written in Si.in are
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created. In addition, disp.yaml file is created. After force
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calculation with the crystal structure in supercell-001.in, it is
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needed to create FORCE_SETS file by
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% phonopy --cp2k -f Si-supercell-001-forces-1_0.xyz
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Here .out files are supposed to contain the forces on atoms calculated
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by CP2K and filenames can be chosen freely. The disp.yaml file has
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to be put in the current directory. Now you can run phonon
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calculation, e.g.,
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% phonopy --cp2k -c Si.inp -p --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --band="1/2 1/2 1/2 0 0 0 1/2 0 1/2"
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@ -0,0 +1,26 @@
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# Example for the CP2K Phonopy interface using bulk silicon
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To create supercells with displacements:
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```console
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$ phonopy --cp2k -c Si.inp -d --dim="2 2 2"
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```
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A perfect 2x2x2 supercell (`Si-supercell-000.inp`) and one 2x2x2 supercells
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(`supercell-001.inp`) of the conventional unit cell written in `Si.inp` are
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created. In addition, a `phonopy_disp.yaml` file is created. After the force
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calculation with the crystal structure in `supercell-001.inp`, it is
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needed to create `FORCE_SETS` file by running:
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```console
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$ phonopy --cp2k -f Si-supercell-001-forces-1_0.xyz
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```
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Here the `.xyz` files are supposed to contain the forces on atoms calculated
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by CP2K.
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To plot the phonon band structure:
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```console
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$ phonopy --cp2k -c Si.inp -p --dim="2 2 2" --pa="0 1/2 1/2 1/2 0 1/2 1/2 1/2 0" --band="1/2 1/2 1/2 0 0 0 1/2 0 1/2"
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```
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@ -2,68 +2,68 @@
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ATOMIC FORCES in [a.u.]
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# Atom Kind Element X Y Z
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1 1 Si -0.00273314 -0.00000000 -0.00000000
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2 1 Si 0.00000278 -0.00000000 -0.00000000
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3 1 Si 0.00001016 -0.00000000 -0.00000000
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4 1 Si 0.00001060 -0.00000000 0.00000000
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5 1 Si 0.00001016 -0.00000000 -0.00000000
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6 1 Si 0.00001060 -0.00000000 0.00000000
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7 1 Si -0.00006163 -0.00000000 -0.00000000
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8 1 Si 0.00000535 -0.00000000 -0.00000000
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9 1 Si -0.00010297 0.00002371 0.00002370
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10 1 Si -0.00000227 0.00000123 0.00000123
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11 1 Si -0.00010290 0.00002332 -0.00002332
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12 1 Si -0.00000223 0.00000123 -0.00000123
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13 1 Si -0.00010290 -0.00002332 0.00002332
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14 1 Si -0.00000223 -0.00000123 0.00000123
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15 1 Si -0.00010297 -0.00002370 -0.00002370
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16 1 Si -0.00000227 -0.00000123 -0.00000123
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17 1 Si 0.00003110 -0.00002346 0.00004240
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18 1 Si 0.00003137 -0.00002377 -0.00004277
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19 1 Si 0.00000152 -0.00000112 -0.00001093
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20 1 Si 0.00000148 -0.00000112 0.00001091
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21 1 Si 0.00003110 0.00002346 -0.00004240
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22 1 Si 0.00003137 0.00002377 0.00004277
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23 1 Si 0.00000152 0.00000111 0.00001093
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24 1 Si 0.00000148 0.00000112 -0.00001091
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25 1 Si 0.00003110 0.00004240 -0.00002346
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26 1 Si 0.00003137 -0.00004277 -0.00002377
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27 1 Si 0.00003110 -0.00004240 0.00002346
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28 1 Si 0.00003137 0.00004277 0.00002377
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29 1 Si 0.00000152 -0.00001093 -0.00000112
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30 1 Si 0.00000148 0.00001091 -0.00000112
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31 1 Si 0.00000152 0.00001093 0.00000112
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32 1 Si 0.00000148 -0.00001091 0.00000112
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33 1 Si -0.00000476 0.00000901 0.00000901
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34 1 Si 0.00004197 0.00000643 0.00000643
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35 1 Si 0.00000657 0.00000620 0.00000727
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36 1 Si -0.00000782 0.00000918 0.00000787
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37 1 Si 0.00000657 0.00000727 0.00000620
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38 1 Si -0.00000782 0.00000787 0.00000918
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39 1 Si 0.00000100 0.00000797 0.00000797
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40 1 Si 0.00069379 0.00042676 0.00042676
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41 1 Si 0.00000100 -0.00000797 -0.00000797
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42 1 Si 0.00069379 -0.00042676 -0.00042676
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43 1 Si 0.00000657 -0.00000727 -0.00000620
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44 1 Si -0.00000782 -0.00000787 -0.00000918
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45 1 Si 0.00000657 -0.00000620 -0.00000727
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46 1 Si -0.00000782 -0.00000918 -0.00000787
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47 1 Si -0.00000476 -0.00000901 -0.00000901
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48 1 Si 0.00004197 -0.00000643 -0.00000643
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49 1 Si -0.00000782 -0.00000780 0.00000929
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50 1 Si 0.00000668 -0.00000723 0.00000622
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51 1 Si 0.00068699 -0.00041420 0.00041420
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52 1 Si 0.00000101 -0.00000787 0.00000787
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53 1 Si 0.00004152 -0.00000632 0.00000632
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54 1 Si -0.00000474 -0.00000896 0.00000896
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55 1 Si -0.00000782 -0.00000929 0.00000780
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56 1 Si 0.00000668 -0.00000622 0.00000723
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57 1 Si -0.00000782 0.00000929 -0.00000780
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58 1 Si 0.00000668 0.00000622 -0.00000723
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59 1 Si 0.00004152 0.00000632 -0.00000632
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60 1 Si -0.00000474 0.00000896 -0.00000896
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61 1 Si 0.00068699 0.00041420 -0.00041420
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62 1 Si 0.00000101 0.00000787 -0.00000787
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63 1 Si -0.00000782 0.00000780 -0.00000929
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64 1 Si 0.00000668 0.00000723 -0.00000622
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SUM OF ATOMIC FORCES 0.00000002 -0.00000000 -0.00000000 0.00000002
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1 1 Si -0.00258246 -0.00000000 0.00000000
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2 1 Si 0.00000263 -0.00000000 -0.00000000
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3 1 Si 0.00000960 -0.00000000 0.00000000
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4 1 Si 0.00001002 -0.00000000 0.00000000
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5 1 Si 0.00000960 -0.00000000 -0.00000000
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6 1 Si 0.00001002 -0.00000000 0.00000000
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7 1 Si -0.00005823 -0.00000000 -0.00000000
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8 1 Si 0.00000505 -0.00000000 -0.00000000
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9 1 Si -0.00009729 0.00002239 0.00002239
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10 1 Si -0.00000214 0.00000116 0.00000116
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11 1 Si -0.00009723 0.00002205 -0.00002205
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12 1 Si -0.00000210 0.00000116 -0.00000116
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13 1 Si -0.00009723 -0.00002205 0.00002205
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14 1 Si -0.00000210 -0.00000116 0.00000116
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15 1 Si -0.00009729 -0.00002239 -0.00002239
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16 1 Si -0.00000214 -0.00000116 -0.00000116
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17 1 Si 0.00002940 -0.00002218 0.00004007
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18 1 Si 0.00002963 -0.00002245 -0.00004040
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19 1 Si 0.00000143 -0.00000105 -0.00001033
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20 1 Si 0.00000140 -0.00000106 0.00001031
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21 1 Si 0.00002940 0.00002218 -0.00004007
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22 1 Si 0.00002963 0.00002245 0.00004040
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23 1 Si 0.00000143 0.00000105 0.00001033
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24 1 Si 0.00000140 0.00000106 -0.00001031
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25 1 Si 0.00002940 0.00004007 -0.00002218
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26 1 Si 0.00002963 -0.00004040 -0.00002245
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27 1 Si 0.00002940 -0.00004007 0.00002218
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28 1 Si 0.00002963 0.00004041 0.00002245
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29 1 Si 0.00000143 -0.00001033 -0.00000105
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30 1 Si 0.00000140 0.00001031 -0.00000106
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31 1 Si 0.00000143 0.00001033 0.00000105
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32 1 Si 0.00000140 -0.00001031 0.00000106
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33 1 Si -0.00000450 0.00000851 0.00000851
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34 1 Si 0.00003964 0.00000607 0.00000607
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35 1 Si 0.00000621 0.00000586 0.00000687
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36 1 Si -0.00000739 0.00000868 0.00000743
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37 1 Si 0.00000621 0.00000687 0.00000586
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38 1 Si -0.00000739 0.00000744 0.00000868
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39 1 Si 0.00000095 0.00000753 0.00000753
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40 1 Si 0.00065536 0.00040290 0.00040290
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41 1 Si 0.00000095 -0.00000753 -0.00000753
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42 1 Si 0.00065536 -0.00040290 -0.00040290
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43 1 Si 0.00000621 -0.00000687 -0.00000586
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44 1 Si -0.00000739 -0.00000744 -0.00000868
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45 1 Si 0.00000621 -0.00000586 -0.00000687
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46 1 Si -0.00000739 -0.00000868 -0.00000743
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47 1 Si -0.00000450 -0.00000851 -0.00000851
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48 1 Si 0.00003964 -0.00000607 -0.00000607
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49 1 Si -0.00000739 -0.00000737 0.00000878
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50 1 Si 0.00000630 -0.00000684 0.00000588
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51 1 Si 0.00064929 -0.00039169 0.00039169
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52 1 Si 0.00000096 -0.00000744 0.00000744
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53 1 Si 0.00003924 -0.00000597 0.00000597
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54 1 Si -0.00000448 -0.00000847 0.00000847
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55 1 Si -0.00000739 -0.00000877 0.00000737
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56 1 Si 0.00000630 -0.00000587 0.00000684
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57 1 Si -0.00000739 0.00000877 -0.00000737
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58 1 Si 0.00000630 0.00000587 -0.00000684
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59 1 Si 0.00003924 0.00000597 -0.00000597
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60 1 Si -0.00000448 0.00000847 -0.00000847
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61 1 Si 0.00064929 0.00039169 -0.00039169
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62 1 Si 0.00000096 0.00000744 -0.00000744
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63 1 Si -0.00000739 0.00000737 -0.00000878
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64 1 Si 0.00000630 0.00000684 -0.00000588
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SUM OF ATOMIC FORCES 0.00000002 0.00000000 0.00000000 0.00000002
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@ -1,204 +0,0 @@
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natom: 64
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displacements:
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- atom: 1
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direction:
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[ 1.0000000000000000, 0.0000000000000000, 0.0000000000000000 ]
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displacement:
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[ 0.0200000000000000, 0.0000000000000000, 0.0000000000000000 ]
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lattice:
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- [ 20.659105641913271, 0.000000000000000, 0.000000000000000 ] # a
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- [ 0.000000000000000, 20.659105641913271, 0.000000000000000 ] # b
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- [ 0.000000000000000, 0.000000000000000, 20.659105641913271 ] # c
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points:
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- symbol: Si # 1
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coordinates: [ 0.437500000000000, 0.437500000000000, 0.437500000000000 ]
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mass: 28.085500
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- symbol: Si # 2
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coordinates: [ 0.937500000000000, 0.437500000000000, 0.437500000000000 ]
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mass: 28.085500
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- symbol: Si # 3
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coordinates: [ 0.437500000000000, 0.937500000000000, 0.437500000000000 ]
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mass: 28.085500
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- symbol: Si # 4
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coordinates: [ 0.937500000000000, 0.937500000000000, 0.437500000000000 ]
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mass: 28.085500
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- symbol: Si # 5
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coordinates: [ 0.437500000000000, 0.437500000000000, 0.937500000000000 ]
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mass: 28.085500
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- symbol: Si # 6
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coordinates: [ 0.937500000000000, 0.437500000000000, 0.937500000000000 ]
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mass: 28.085500
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- symbol: Si # 7
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coordinates: [ 0.437500000000000, 0.937500000000000, 0.937500000000000 ]
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mass: 28.085500
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- symbol: Si # 8
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coordinates: [ 0.937500000000000, 0.937500000000000, 0.937500000000000 ]
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mass: 28.085500
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- symbol: Si # 9
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coordinates: [ 0.437500000000000, 0.187500000000000, 0.187500000000000 ]
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mass: 28.085500
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- symbol: Si # 10
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coordinates: [ 0.937500000000000, 0.187500000000000, 0.187500000000000 ]
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mass: 28.085500
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- symbol: Si # 11
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coordinates: [ 0.437500000000000, 0.687500000000000, 0.187500000000000 ]
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mass: 28.085500
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- symbol: Si # 12
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coordinates: [ 0.937500000000000, 0.687500000000000, 0.187500000000000 ]
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mass: 28.085500
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- symbol: Si # 13
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coordinates: [ 0.437500000000000, 0.187500000000000, 0.687500000000000 ]
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mass: 28.085500
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- symbol: Si # 14
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coordinates: [ 0.937500000000000, 0.187500000000000, 0.687500000000000 ]
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mass: 28.085500
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- symbol: Si # 15
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coordinates: [ 0.437500000000000, 0.687500000000000, 0.687500000000000 ]
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mass: 28.085500
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- symbol: Si # 16
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coordinates: [ 0.937500000000000, 0.687500000000000, 0.687500000000000 ]
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mass: 28.085500
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- symbol: Si # 17
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coordinates: [ 0.187500000000000, 0.437500000000000, 0.187500000000000 ]
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mass: 28.085500
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- symbol: Si # 18
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coordinates: [ 0.687500000000000, 0.437500000000000, 0.187500000000000 ]
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mass: 28.085500
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- symbol: Si # 19
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coordinates: [ 0.187500000000000, 0.937500000000000, 0.187500000000000 ]
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mass: 28.085500
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- symbol: Si # 20
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coordinates: [ 0.687500000000000, 0.937500000000000, 0.187500000000000 ]
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mass: 28.085500
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- symbol: Si # 21
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coordinates: [ 0.187500000000000, 0.437500000000000, 0.687500000000000 ]
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mass: 28.085500
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- symbol: Si # 22
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coordinates: [ 0.687500000000000, 0.437500000000000, 0.687500000000000 ]
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mass: 28.085500
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- symbol: Si # 23
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coordinates: [ 0.187500000000000, 0.937500000000000, 0.687500000000000 ]
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mass: 28.085500
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- symbol: Si # 24
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coordinates: [ 0.687500000000000, 0.937500000000000, 0.687500000000000 ]
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mass: 28.085500
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- symbol: Si # 25
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coordinates: [ 0.187500000000000, 0.187500000000000, 0.437500000000000 ]
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mass: 28.085500
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- symbol: Si # 26
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coordinates: [ 0.687500000000000, 0.187500000000000, 0.437500000000000 ]
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mass: 28.085500
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- symbol: Si # 27
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coordinates: [ 0.187500000000000, 0.687500000000000, 0.437500000000000 ]
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mass: 28.085500
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- symbol: Si # 28
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coordinates: [ 0.687500000000000, 0.687500000000000, 0.437500000000000 ]
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mass: 28.085500
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- symbol: Si # 29
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coordinates: [ 0.187500000000000, 0.187500000000000, 0.937500000000000 ]
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mass: 28.085500
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- symbol: Si # 30
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coordinates: [ 0.687500000000000, 0.187500000000000, 0.937500000000000 ]
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mass: 28.085500
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- symbol: Si # 31
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coordinates: [ 0.187500000000000, 0.687500000000000, 0.937500000000000 ]
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mass: 28.085500
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- symbol: Si # 32
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coordinates: [ 0.687500000000000, 0.687500000000000, 0.937500000000000 ]
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mass: 28.085500
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- symbol: Si # 33
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coordinates: [ 0.062500000000000, 0.062500000000000, 0.062500000000000 ]
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mass: 28.085500
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- symbol: Si # 34
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coordinates: [ 0.562500000000000, 0.062500000000000, 0.062500000000000 ]
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mass: 28.085500
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- symbol: Si # 35
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coordinates: [ 0.062500000000000, 0.562500000000000, 0.062500000000000 ]
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mass: 28.085500
|
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- symbol: Si # 36
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coordinates: [ 0.562500000000000, 0.562500000000000, 0.062500000000000 ]
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mass: 28.085500
|
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- symbol: Si # 37
|
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coordinates: [ 0.062500000000000, 0.062500000000000, 0.562500000000000 ]
|
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mass: 28.085500
|
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- symbol: Si # 38
|
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coordinates: [ 0.562500000000000, 0.062500000000000, 0.562500000000000 ]
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mass: 28.085500
|
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- symbol: Si # 39
|
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coordinates: [ 0.062500000000000, 0.562500000000000, 0.562500000000000 ]
|
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mass: 28.085500
|
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- symbol: Si # 40
|
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coordinates: [ 0.562500000000000, 0.562500000000000, 0.562500000000000 ]
|
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mass: 28.085500
|
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- symbol: Si # 41
|
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coordinates: [ 0.062500000000000, 0.312500000000000, 0.312500000000000 ]
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mass: 28.085500
|
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- symbol: Si # 42
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coordinates: [ 0.562500000000000, 0.312500000000000, 0.312500000000000 ]
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mass: 28.085500
|
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- symbol: Si # 43
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coordinates: [ 0.062500000000000, 0.812500000000000, 0.312500000000000 ]
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mass: 28.085500
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- symbol: Si # 44
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coordinates: [ 0.562500000000000, 0.812500000000000, 0.312500000000000 ]
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mass: 28.085500
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- symbol: Si # 45
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coordinates: [ 0.062500000000000, 0.312500000000000, 0.812500000000000 ]
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mass: 28.085500
|
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- symbol: Si # 46
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coordinates: [ 0.562500000000000, 0.312500000000000, 0.812500000000000 ]
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mass: 28.085500
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- symbol: Si # 47
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coordinates: [ 0.062500000000000, 0.812500000000000, 0.812500000000000 ]
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mass: 28.085500
|
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- symbol: Si # 48
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coordinates: [ 0.562500000000000, 0.812500000000000, 0.812500000000000 ]
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mass: 28.085500
|
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- symbol: Si # 49
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coordinates: [ 0.312500000000000, 0.062500000000000, 0.312500000000000 ]
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mass: 28.085500
|
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- symbol: Si # 50
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coordinates: [ 0.812500000000000, 0.062500000000000, 0.312500000000000 ]
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mass: 28.085500
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- symbol: Si # 51
|
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coordinates: [ 0.312500000000000, 0.562500000000000, 0.312500000000000 ]
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mass: 28.085500
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- symbol: Si # 52
|
||||
coordinates: [ 0.812500000000000, 0.562500000000000, 0.312500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 53
|
||||
coordinates: [ 0.312500000000000, 0.062500000000000, 0.812500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 54
|
||||
coordinates: [ 0.812500000000000, 0.062500000000000, 0.812500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 55
|
||||
coordinates: [ 0.312500000000000, 0.562500000000000, 0.812500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 56
|
||||
coordinates: [ 0.812500000000000, 0.562500000000000, 0.812500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 57
|
||||
coordinates: [ 0.312500000000000, 0.312500000000000, 0.062500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 58
|
||||
coordinates: [ 0.812500000000000, 0.312500000000000, 0.062500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 59
|
||||
coordinates: [ 0.312500000000000, 0.812500000000000, 0.062500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 60
|
||||
coordinates: [ 0.812500000000000, 0.812500000000000, 0.062500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 61
|
||||
coordinates: [ 0.312500000000000, 0.312500000000000, 0.562500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 62
|
||||
coordinates: [ 0.812500000000000, 0.312500000000000, 0.562500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 63
|
||||
coordinates: [ 0.312500000000000, 0.812500000000000, 0.562500000000000 ]
|
||||
mass: 28.085500
|
||||
- symbol: Si # 64
|
||||
coordinates: [ 0.812500000000000, 0.812500000000000, 0.562500000000000 ]
|
||||
mass: 28.085500
|
||||
|
|
@ -99,7 +99,9 @@ def write_supercells_with_displacements(interface_mode,
|
|||
optional_structure_info[1])
|
||||
elif interface_mode == 'cp2k':
|
||||
from phonopy.interface.cp2k import write_supercells_with_displacements
|
||||
write_supercells_with_displacements(supercell, cells_with_disps)
|
||||
write_supercells_with_displacements(supercell,
|
||||
cells_with_disps,
|
||||
optional_structure_info)
|
||||
elif interface_mode == 'crystal':
|
||||
from phonopy.interface.crystal import (
|
||||
write_supercells_with_displacements)
|
||||
|
|
@ -165,8 +167,8 @@ def read_crystal_structure(filename=None,
|
|||
return unitcell, (cell_filename, atypes)
|
||||
elif interface_mode == 'cp2k':
|
||||
from phonopy.interface.cp2k import read_cp2k
|
||||
unitcell = read_cp2k(cell_filename)
|
||||
return unitcell, (cell_filename,)
|
||||
unitcell, config_tree = read_cp2k(cell_filename)
|
||||
return unitcell, (cell_filename, config_tree)
|
||||
elif interface_mode == 'crystal':
|
||||
from phonopy.interface.crystal import read_crystal
|
||||
unitcell, conv_numbers = read_crystal(cell_filename)
|
||||
|
|
@ -216,7 +218,7 @@ def get_default_supercell_filename(interface_mode):
|
|||
elif interface_mode == 'siesta':
|
||||
return "supercell.fdf"
|
||||
elif interface_mode == 'cp2k':
|
||||
return "supercell.inp"
|
||||
return None # CP2K interface generates filenames based on original project name
|
||||
elif interface_mode == 'crystal':
|
||||
return None # supercell.ext can not be parsed by crystal interface.
|
||||
elif interface_mode == 'dftbp':
|
||||
|
|
@ -228,12 +230,9 @@ def get_default_supercell_filename(interface_mode):
|
|||
|
||||
|
||||
def get_default_displacement_distance(interface_mode):
|
||||
if interface_mode in ('wien2k', 'abinit', 'elk', 'qe', 'siesta', 'cp2k',
|
||||
'turbomole'):
|
||||
if interface_mode in ('wien2k', 'abinit', 'elk', 'qe', 'siesta', 'turbomole'):
|
||||
displacement_distance = 0.02
|
||||
elif interface_mode == 'crystal':
|
||||
displacement_distance = 0.01
|
||||
else: # default or vasp
|
||||
else: # default or vasp, crystal, cp2k
|
||||
displacement_distance = 0.01
|
||||
return displacement_distance
|
||||
|
||||
|
|
@ -251,6 +250,7 @@ def get_default_physical_units(interface_mode=None):
|
|||
CRYSTAL : eV, Angstrom, AMU, eV/Angstroem
|
||||
DFTB+ : hartree, au, AMU hartree/au
|
||||
TURBOMOLE : hartree, au, AMU, hartree/au
|
||||
CP2K : hartree, Angstrom, AMU, hartree/au
|
||||
|
||||
"""
|
||||
|
||||
|
|
@ -302,9 +302,9 @@ def get_default_physical_units(interface_mode=None):
|
|||
units['length_unit'] = 'au'
|
||||
elif interface_mode == 'cp2k':
|
||||
units['factor'] = CP2KToTHz
|
||||
units['nac_factor'] = Hartree / Bohr # in a.u.
|
||||
units['distance_to_A'] = Bohr
|
||||
units['force_constants_unit'] = 'hartree/au^2'
|
||||
units['nac_factor'] = None # not implemented
|
||||
units['distance_to_A'] = 1.0
|
||||
units['force_constants_unit'] = 'hartree/Angstrom.au'
|
||||
units['length_unit'] = 'Angstrom'
|
||||
elif interface_mode == 'crystal':
|
||||
units['factor'] = CrystalToTHz
|
||||
|
|
@ -475,7 +475,8 @@ def get_force_constant_conversion_factor(unit, interface_mode):
|
|||
'eV/Angstrom.au': 1 / Bohr,
|
||||
'Ry/au^2': Rydberg / Bohr ** 2,
|
||||
'mRy/au^2': Rydberg / Bohr ** 2 / 1000,
|
||||
'hartree/au^2': Hartree / Bohr ** 2}
|
||||
'hartree/au^2': Hartree / Bohr ** 2,
|
||||
'hartree/Angstrom.au': Hartree / Bohr }
|
||||
if default_unit not in factor_to_eVperA2:
|
||||
msg = "Force constant conversion for %s unit is not implemented."
|
||||
raise NotImplementedError(msg)
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
# vim: set fileencoding=utf-8 :
|
||||
# Copyright (C) 2017 Tiziano Müller
|
||||
# Copyright (C) 2017-2019 Tiziano Müller
|
||||
# All rights reserved.
|
||||
#
|
||||
# This file is part of phonopy.
|
||||
|
|
@ -33,124 +33,191 @@
|
|||
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
|
||||
# POSSIBILITY OF SUCH DAMAGE.
|
||||
|
||||
from __future__ import print_function
|
||||
|
||||
import sys
|
||||
from fractions import Fraction
|
||||
from os import path
|
||||
import numpy as np
|
||||
|
||||
from phonopy.file_IO import collect_forces
|
||||
from phonopy.file_IO import iter_collect_forces
|
||||
from phonopy.interface.vasp import (check_forces, get_drift_forces)
|
||||
from phonopy.structure.atoms import (PhonopyAtoms, symbol_map)
|
||||
from phonopy.units import Bohr
|
||||
|
||||
|
||||
def parse_set_of_forces(num_atoms, forces_filenames, verbose=True):
|
||||
hook = '# Atom Kind Element'
|
||||
|
||||
force_sets = []
|
||||
|
||||
for i, filename in enumerate(forces_filenames):
|
||||
if verbose:
|
||||
sys.stdout.write("%d. " % (i + 1))
|
||||
|
||||
with open(filename) as fhandle:
|
||||
cp2k_forces = collect_forces(fhandle, num_atoms, hook, [3, 4, 5])
|
||||
if check_forces(cp2k_forces, num_atoms, filename, verbose=verbose):
|
||||
drift_force = get_drift_forces(cp2k_forces,
|
||||
filename=filename,
|
||||
verbose=verbose)
|
||||
force_sets.append(np.array(cp2k_forces) - drift_force)
|
||||
else:
|
||||
return [] # if one file is invalid, the whole thing is broken
|
||||
forces = iter_collect_forces(filename, num_atoms, '# Atom Kind Element', [3, 4, 5])
|
||||
|
||||
if not check_forces(forces, num_atoms, filename, verbose=verbose):
|
||||
return [] # if one file is invalid, the whole thing is broken
|
||||
|
||||
drift_force = get_drift_forces(forces, filename=filename, verbose=verbose)
|
||||
force_sets.append(np.array(forces) - drift_force)
|
||||
|
||||
return force_sets
|
||||
|
||||
|
||||
def read_cp2k(filename):
|
||||
from cp2k_tools.parser import CP2KInputParser
|
||||
from cp2k_input_tools.parser import CP2KInputParser
|
||||
|
||||
with open(filename) as fhandle:
|
||||
parser = CP2KInputParser()
|
||||
cp2k_in = parser.parse(fhandle)
|
||||
tree = parser.parse(fhandle)
|
||||
|
||||
cp2k_cell = cp2k_in['force_eval']['subsys']['cell']
|
||||
cp2k_coord = cp2k_in['force_eval']['subsys']['coord']
|
||||
try:
|
||||
subsys = tree['+force_eval'][0]['+subsys']
|
||||
cp2k_cell = subsys['+cell']
|
||||
except IndexError:
|
||||
raise RuntimeError("could not find a FORCE_EVAL/SUBSYS/CELL section in the given CP2K input file")
|
||||
|
||||
if 'abc' in cp2k_cell:
|
||||
unit = '[angstrom]' # CP2K default unit
|
||||
unit_cell = np.eye(3)
|
||||
if isinstance(cp2k_cell['abc'][0], str):
|
||||
unit = cp2k_cell['abc'][0]
|
||||
unit_cell *= cp2k_cell['abc'][1:]
|
||||
if len(tree['+force_eval']) > 1:
|
||||
raise NotImplementedError("the given CP2K input file contains multiple FORCE_EVAL sections, which is not (yet) supported")
|
||||
|
||||
# CP2K can get its cell information in two ways:
|
||||
# - A, B, C: cell vectors
|
||||
# - ABC: scaling of cell vectors, ALPHA_BETA_GAMMA: angles between the cell vectors
|
||||
# We'll parse either of them, but only write A, B, C
|
||||
if 'a' in cp2k_cell:
|
||||
# unit vectors given
|
||||
unit_cell = np.array([
|
||||
cp2k_cell['a'],
|
||||
cp2k_cell['b'],
|
||||
cp2k_cell['c'],
|
||||
])
|
||||
elif 'abc' in cp2k_cell:
|
||||
# length of unit vectors given
|
||||
if 'alpha_beta_gamma' in cp2k_cell:
|
||||
# if we also have the angles, construct the cell
|
||||
|
||||
alpha, beta, gamma = cp2k_cell.pop('alpha_beta_gamma')
|
||||
|
||||
cos_alpha = np.cos(alpha)
|
||||
cos_beta = np.cos(beta)
|
||||
cos_gamma = np.cos(gamma)
|
||||
sin_gamma = np.sin(gamma)
|
||||
|
||||
unit_cell = np.array([
|
||||
[1., 0., 0.],
|
||||
[cos_gamma, sin_gamma, 0.],
|
||||
[
|
||||
cos_beta,
|
||||
(cos_alpha-cos_gamma*cos_beta)/sin_gamma,
|
||||
np.sqrt(1.-cos_beta**2-((cos_alpha-cos_gamma*cos_beta)/sin_gamma)**2),
|
||||
],
|
||||
])
|
||||
else:
|
||||
unit_cell *= cp2k_cell['abc']
|
||||
unit_cell = np.eye(3)
|
||||
|
||||
if unit == '[angstrom]':
|
||||
unit_cell /= Bohr # phonopy expects the lattice to be in Bohr
|
||||
else:
|
||||
raise NotImplementedError("unit scaling for other units than angstrom not yet implemented")
|
||||
a, b, c = cp2k_cell.pop('abc') # remove them from the tree since we pass it along
|
||||
|
||||
unit_cell[0,:] *= a
|
||||
unit_cell[1,:] *= b
|
||||
unit_cell[2,:] *= c
|
||||
|
||||
if '+cell_ref' in cp2k_cell:
|
||||
print("WARNING: the &CELL_REF section must be manually adjusted")
|
||||
|
||||
cp2k_coord = subsys['+coord']
|
||||
|
||||
numbers = []
|
||||
positions = []
|
||||
|
||||
for coordline in cp2k_coord['*']:
|
||||
# coordinates are a series of strings according to the CP2K schema
|
||||
fields = coordline.split()
|
||||
numbers += [symbol_map[fields[0]]]
|
||||
# positions can also be fractions
|
||||
positions += [[float(Fraction(f)) for f in fields[1:4]]]
|
||||
|
||||
if cp2k_coord.get('scaled', False): # the keyword can be unavailable, true or false
|
||||
return (PhonopyAtoms(numbers=numbers, cell=unit_cell, scaled_positions=positions), tree)
|
||||
else:
|
||||
raise NotImplementedError("unit cell can only be specified via ABC")
|
||||
|
||||
# the keyword can be unavailable, true, false or None, with unavailable=false, None=true
|
||||
scaled_coords = cp2k_coord.get('scaled', False) is not False
|
||||
|
||||
if not scaled_coords:
|
||||
raise NotImplementedError("only scaled coordinates are currently supported")
|
||||
|
||||
|
||||
numbers = [symbol_map[e[0]] for e in cp2k_coord['*']]
|
||||
positions = [e[1:] for e in cp2k_coord['*']]
|
||||
|
||||
return PhonopyAtoms(numbers=numbers, cell=unit_cell, scaled_positions=positions)
|
||||
|
||||
|
||||
def write_cp2k(filename, cell):
|
||||
with open(filename, 'w') as fhandle:
|
||||
fhandle.write(get_cp2k_structure(cell))
|
||||
return (PhonopyAtoms(numbers=numbers, cell=unit_cell, positions=positions), tree)
|
||||
|
||||
|
||||
def write_supercells_with_displacements(supercell,
|
||||
cells_with_displacements,
|
||||
optional_structure_info,
|
||||
pre_filename="supercell",
|
||||
width=3):
|
||||
|
||||
write_cp2k("supercell.inp", supercell)
|
||||
orig_fname, tree = optional_structure_info
|
||||
|
||||
fbase, fext = path.splitext(orig_fname)
|
||||
pbase = tree["+global"]["project_name"]
|
||||
|
||||
supercell_ref_name = "{}-supercell{}".format(fbase, fext)
|
||||
with open(supercell_ref_name, 'w') as fhandle:
|
||||
fhandle.write("""\
|
||||
# Generated by Phonopy, based on {fname}
|
||||
# Original configuration with the generated supercell for comparison
|
||||
""".format(fname=orig_fname))
|
||||
write_cp2k(fhandle, "{}-supercell".format(pbase), supercell, tree)
|
||||
|
||||
for i, cell in enumerate(cells_with_displacements):
|
||||
filename = "{pre_filename}-{0:0{width}}.inp".format(
|
||||
suffix = "{pre_filename}-{0:0{width}}".format(
|
||||
i + 1,
|
||||
pre_filename=pre_filename,
|
||||
width=width)
|
||||
write_cp2k(filename, cell)
|
||||
|
||||
with open("{}-{}{}".format(fbase, suffix, fext), 'w') as fhandle:
|
||||
fhandle.write("""\
|
||||
# Generated by Phonopy, based on {fname}
|
||||
# Merged configuration with displacements
|
||||
""".format(fname=orig_fname))
|
||||
write_cp2k(fhandle, "{}-{}".format(pbase, suffix), cell, tree)
|
||||
|
||||
|
||||
def get_cp2k_structure(atoms):
|
||||
"""Convert the atoms structure to a CP2K input file skeleton string"""
|
||||
def write_cp2k(fhandle, project_name, atoms, tree):
|
||||
"""Merge the new the atoms structure with the configuration tree to a new CP2K input file
|
||||
|
||||
from cp2k_tools.generator import dict2cp2k
|
||||
:param fhandle: open file handle to which the routine will write to
|
||||
:param project_name: the project name to use (CP2K uses that as prefix for generated files)i
|
||||
:param atoms: the Atoms objects to use
|
||||
:param tree: the configuration tree as returned from CP2KInputParser
|
||||
"""
|
||||
|
||||
# CP2K's default unit is angstrom, convert it, but still declare it explictly:
|
||||
cp2k_cell = {sym: ('[angstrom]',) + tuple(coords) for sym, coords in zip(('a', 'b', 'c'), atoms.get_cell()*Bohr)}
|
||||
cp2k_cell['periodic'] = 'XYZ' # anything else does not make much sense
|
||||
cp2k_coord = {
|
||||
'scaled': True,
|
||||
'*': [[sym] + list(coord) for sym, coord in zip(atoms.get_chemical_symbols(), atoms.get_scaled_positions())],
|
||||
}
|
||||
from cp2k_input_tools.generator import CP2KInputGenerator
|
||||
generator = CP2KInputGenerator()
|
||||
|
||||
return dict2cp2k(
|
||||
{
|
||||
'global': {
|
||||
'run_type': 'ENERGY_FORCE',
|
||||
},
|
||||
'force_eval': {
|
||||
'subsys': {
|
||||
'cell': cp2k_cell,
|
||||
'coord': cp2k_coord,
|
||||
},
|
||||
'print': {
|
||||
'forces': {
|
||||
'filename': 'forces',
|
||||
},
|
||||
},
|
||||
},
|
||||
tree['+global']['run_type'] = 'ENERGY_FORCE'
|
||||
tree['+global']['project_name'] = project_name
|
||||
|
||||
force_eval = tree['+force_eval'][0]
|
||||
subsys = force_eval['+subsys']
|
||||
|
||||
# if the original input contained scaled positions, continue with scaled positions
|
||||
if subsys['+coord'].get('scaled', False):
|
||||
cp2k_coord = {
|
||||
'scaled': True,
|
||||
'*': ["{sym} {x} {y} {z}".format(sym=sym, x=coord[0], y=coord[1], z=coord[2])
|
||||
for sym, coord in zip(atoms.get_chemical_symbols(), atoms.get_scaled_positions())],
|
||||
}
|
||||
)
|
||||
# ... otherwise use absolute positions
|
||||
else:
|
||||
cp2k_coord = {
|
||||
'*': ["{sym} {x} {y} {z}".format(sym=sym, x=coord[0], y=coord[1], z=coord[2])
|
||||
for sym, coord in zip(atoms.get_chemical_symbols(), atoms.get_positions())],
|
||||
}
|
||||
|
||||
subsys['+cell']['a'] = list(atoms.get_cell()[0])
|
||||
subsys['+cell']['b'] = list(atoms.get_cell()[1])
|
||||
subsys['+cell']['c'] = list(atoms.get_cell()[2])
|
||||
subsys['+cell']['periodic'] = 'XYZ' # anything else does not make much sense
|
||||
|
||||
subsys['+coord'] = cp2k_coord # overwriting the coordinates
|
||||
|
||||
if not '+print' in force_eval:
|
||||
force_eval['+print'] = {}
|
||||
if not '+forces' in force_eval['+print']:
|
||||
force_eval['+print']['+forces'] = {}
|
||||
force_eval['+print']['+forces']['filename'] = "forces" # uses the project name as base with 'forces' as suffix
|
||||
|
||||
for line in generator.line_iter(tree):
|
||||
fhandle.write("{line}\n".format(line=line))
|
||||
|
|
|
|||
|
|
@ -66,7 +66,7 @@ AbinitToTHz = sqrt(EV/(AMU*Bohr))/Angstrom/(2*pi)/1e12 # [THz] 21.49068
|
|||
PwscfToTHz = sqrt(Rydberg*EV/AMU)/(Bohr*1e-10)/(2*pi)/1e12 # [THz] 108.97077
|
||||
ElkToTHz = sqrt(Hartree*EV/AMU)/(Bohr*1e-10)/(2*pi)/1e12 # [THz] 154.10794
|
||||
SiestaToTHz = sqrt(EV/(AMU*Bohr))/Angstrom/(2*pi)/1e12 # [THz] 21.49068
|
||||
CP2KToTHz = ElkToTHz # CP2K uses a.u. units (Hartree/Bohr)
|
||||
CP2KToTHz = sqrt(Hartree*EV/(AMU*Bohr))/Angstrom/(2*pi)/1e12 # CP2K uses a.u. for forces but Angstrom for distances
|
||||
CrystalToTHz = VaspToTHz
|
||||
DftbpToTHz = sqrt(Hartree*EV/AMU)/(Bohr*1e-10)/(2*pi)/1e12 # [THz] 154.10794344
|
||||
dftbpToBohr = 0.188972598857892E+01
|
||||
|
|
|
|||
1
setup.py
1
setup.py
|
|
@ -182,6 +182,7 @@ if __name__ == '__main__':
|
|||
url='http://atztogo.github.io/phonopy/',
|
||||
packages=packages_phonopy,
|
||||
install_requires=['numpy', 'PyYAML', 'matplotlib', 'h5py'],
|
||||
extras_require={'cp2k': ['cp2k-input-tools']},
|
||||
provides=['phonopy'],
|
||||
scripts=scripts_phonopy,
|
||||
ext_modules=ext_modules_phonopy,
|
||||
|
|
|
|||
Loading…
Reference in New Issue