mirror of
https://github.com/triqs/dft_tools
synced 2024-12-22 04:13:47 +01:00
* Restructured the directory structure * Added some half-day long development including tests
This commit is contained in:
Oleg Peil
Michel Ferrero
parent
e85d3b4f2b
commit
bd6198d264
@ -1,74 +0,0 @@
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2 2 1 2
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0.1333597E+02 0.2987800E-09 0.2987800E-09 0.2987800E-09 0.5000000E-15
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1.000000000000000E-004
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CAR
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V
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22 4 15
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0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3703704E-01
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1 -31.708596 -31.708596
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2 -31.708596 -31.708596
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3 -31.708596 -31.708596
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4 -31.061475 -31.061475
|
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5 -31.061475 -31.061475
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||||
6 -31.061475 -31.061475
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7 -0.811953 -0.811953
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8 2.607665 2.607665
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9 2.607665 2.607665
|
||||
10 6.002735 6.002735
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11 6.002735 6.002735
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12 6.002735 6.002735
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13 8.013630 8.013630
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14 8.013630 8.013630
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15 9.361252 9.361252
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||||
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0.3333333E+00 0.0000000E+00 0.0000000E+00 0.2222222E+00
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||||
1 -31.682851 -31.682851
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2 -31.539793 -31.539793
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3 -31.539793 -31.539793
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4 -31.363786 -31.363786
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5 -31.215960 -31.215960
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6 -31.215960 -31.215960
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7 1.216017 1.216017
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8 3.394994 3.394994
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9 3.771669 3.771669
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10 6.050595 6.050595
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11 6.050595 6.050595
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12 6.457025 6.457025
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13 6.771661 6.771661
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14 7.383619 7.383619
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15 7.383620 7.383620
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0.3333333E+00 0.3333333E+00 0.0000000E+00 0.4444444E+00
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1 -31.935665 -31.935665
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2 -31.782518 -31.782518
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3 -31.447103 -31.447103
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4 -31.284953 -31.284953
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5 -31.234384 -31.234384
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6 -31.067231 -31.067231
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7 2.201004 2.201004
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8 3.123182 3.123182
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9 4.809697 4.809697
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10 5.123957 5.123957
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11 5.357025 5.357025
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12 5.853431 5.853431
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13 7.260017 7.260017
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14 7.862532 7.862532
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15 8.230907 8.230907
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0.3333333E+00 0.3333333E+00 0.3333333E+00 0.2962963E+00
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1 -31.808727 -31.808727
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2 -31.713049 -31.713049
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3 -31.713049 -31.713049
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4 -31.278227 -31.278227
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5 -31.278227 -31.278227
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6 -31.179331 -31.179331
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7 3.831291 3.831291
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8 3.998572 3.998572
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9 4.466211 4.466211
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10 4.466211 4.466211
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11 4.724276 4.724276
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12 4.724276 4.724276
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13 8.230309 8.230309
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14 8.253908 8.253831
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15 8.292606 8.292606
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File diff suppressed because it is too large
Load Diff
@ -1,29 +0,0 @@
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LuNiO3, low-T, P2_1/n
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1.0
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5.1234998703 0.0000000000 0.0000000000
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0.0000000000 5.5089001656 0.0000000000
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-0.0166880521 0.0000000000 7.3551808822
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Lu Ni O
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4 4 12
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Cartesian
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5.00246185 0.42418531 1.86086070
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0.10434997 5.08471473 5.49431996
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2.67444393 3.17863552 1.81672974
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2.43236789 2.33026481 5.53845136
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2.56174994 0.00000000 0.00000000
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-0.00834403 2.75445008 3.67759044
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2.55340591 0.00000000 3.67759044
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0.00000000 2.75445008 0.00000000
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0.56002379 2.54896816 1.79539968
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4.54678788 2.95993201 5.55978141
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1.99338212 5.30341824 1.88219076
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3.11342985 0.20548193 5.47298991
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3.55122302 1.72814193 0.39644425
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1.55558880 3.78075840 6.95873661
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4.12568276 4.48259185 3.28114617
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0.98112906 1.02630815 4.07403471
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0.93260966 1.11059427 6.94181952
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4.17420208 4.39830581 0.41336136
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1.60410812 3.86504444 4.09095181
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3.50270370 1.64385573 3.26422908
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@ -1,29 +0,0 @@
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LuNiO3, low-T, P2_1/n
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1.0
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5.1234998703 0.0000000000 0.0000000000
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0.0000000000 5.5089001656 0.0000000000
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-0.0166880521 0.0000000000 7.3551808822
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Lu Ni O
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4 4 12
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Kartesian
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5.00246185 0.42418531 1.86086070
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0.10434997 5.08471473 5.49431996
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2.67444393 3.17863552 1.81672974
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2.43236789 2.33026481 5.53845136
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2.56174994 0.00000000 0.00000000
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-0.00834403 2.75445008 3.67759044
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2.55340591 0.00000000 3.67759044
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0.00000000 2.75445008 0.00000000
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0.56002379 2.54896816 1.79539968
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4.54678788 2.95993201 5.55978141
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1.99338212 5.30341824 1.88219076
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3.11342985 0.20548193 5.47298991
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3.55122302 1.72814193 0.39644425
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1.55558880 3.78075840 6.95873661
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4.12568276 4.48259185 3.28114617
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0.98112906 1.02630815 4.07403471
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0.93260966 1.11059427 6.94181952
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4.17420208 4.39830581 0.41336136
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1.60410812 3.86504444 4.09095181
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3.50270370 1.64385573 3.26422908
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@ -1,28 +0,0 @@
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LuNiO3, low-T, P2_1/n
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1.0
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5.1234998703 0.0000000000 0.0000000000
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0.0000000000 5.5089001656 0.0000000000
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-0.0166880521 0.0000000000 7.3551808822
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Lu Ni O
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4 4 12
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Direct
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0.977199972 0.077000000 0.252999991
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0.022800028 0.922999978 0.746999979
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0.522800028 0.577000022 0.247000009
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0.477199972 0.423000008 0.753000021
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0.500000000 0.000000000 0.000000000
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0.000000000 0.500000000 0.500000000
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0.500000000 0.000000000 0.500000000
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0.000000000 0.500000000 0.000000000
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0.110100001 0.462700009 0.244100004
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0.889899969 0.537299991 0.755900025
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0.389899999 0.962700009 0.255899996
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0.610100031 0.037299991 0.744099975
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0.693300009 0.313699991 0.053900000
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0.306699991 0.686300039 0.946099997
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0.806699991 0.813699961 0.446099997
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0.193300009 0.186300009 0.553900003
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0.185100004 0.201600000 0.943799973
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0.814899981 0.798399985 0.056200027
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0.314899981 0.701600015 0.556200027
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0.685100019 0.298399985 0.443799973
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@ -1,4 +1,5 @@
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makefile
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Makefile
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*.so
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*.o
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*.pyc
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@ -5,5 +5,4 @@ LIB_FLAGS=-L/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/
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c_plocar_io.so: c_plocar_io.c
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$(CC) $< -fPIC -shared -o $@ $(INC_FLAGS) $(LIB_FLAGS) -lpython2.7
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cp $@ ..
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8
python/converters/vasp/c/plocar_io/makefile.linux
Normal file
8
python/converters/vasp/c/plocar_io/makefile.linux
Normal file
@ -0,0 +1,8 @@
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CC=gcc
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INC_FLAGS=-I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include/numpy
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LIB_FLAGS=-L/usr/lib/python2.7
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c_plocar_io.so: c_plocar_io.c
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$(CC) $< -fPIC -shared -o $@ $(INC_FLAGS) $(LIB_FLAGS) -lpython2.7
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@ -1,8 +1,12 @@
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r"""
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Module for parsing and checking an input config-file.
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"""
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import ConfigParser
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import numpy as np
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import re
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import sys
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import itertools as it
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import vaspio
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def issue_warning(message):
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@ -12,6 +16,7 @@ def issue_warning(message):
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print
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print " !!! WARNING !!!: " + message
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print
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################################################################################
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################################################################################
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#
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@ -34,23 +39,6 @@ class ConfigParameters:
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1. internal name of a parameter
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2. function used to convert an input string into data for a given parameter
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"""
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self.sh_required = {
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'ions': ('ion_list', self.parse_ion_list),
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'lshell': ('lshell', int)}
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self.sh_optional = {
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'rtransform': ('tmatrix', lambda s: self.parse_tmatrix(s, real=True)),
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'ctransform': ('tmatrix', lambda s: self.parse_tmatrix(s, real=False))}
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self.gr_required = {
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'emin': ('emin', float),
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'emax': ('emax', float)}
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self.gr_optional = {
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'normalize' : ('normalize', self.parse_logical),
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'normion' : ('normion', self.parse_logical)}
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################################################################################
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#
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# __init__()
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@ -58,10 +46,29 @@ class ConfigParameters:
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################################################################################
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def __init__(self, input_filename, verbosity=1):
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self.verbosity = verbosity
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self.cp = ConfigParser.ConfigParser()
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self.cp = ConfigParser.SafeConfigParser()
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self.cp.readfp(open(input_filename, 'r'))
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self.conf_pars = {}
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self.parameters = {}
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self.sh_required = {
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'ions': ('ion_list', self.parse_string_ion_list),
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'lshell': ('lshell', int)}
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self.sh_optional = {
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'rtransform': ('tmatrix', lambda s: self.parse_string_tmatrix(s, real=True)),
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'ctransform': ('tmatrix', lambda s: self.parse_string_tmatrix(s, real=False))}
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self.gr_required = {
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'shells': ('shells', lambda s: map(int, s.split())),
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'emin': ('emin', float),
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'emax': ('emax', float)}
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self.gr_optional = {
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'normalize' : ('normalize', self.parse_string_logical),
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'normion' : ('normion', self.parse_string_logical)}
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#
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# Special parsers
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@ -75,13 +82,25 @@ class ConfigParameters:
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"""
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The ion list accepts two formats:
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1). A list of ion indices according to POSCAR.
|
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The list can be defined as a range '9..20'.
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2). An element name, in which case all ions with
|
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this name are included.
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The second option requires an input from POSCAR file.
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"""
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# First check if a range is given
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patt = '([0-9]+)\.\.([0-9]+)'
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match = re.match(patt, par_str)
|
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if match:
|
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i1, i2 = tuple(map(int, match.groups()[:2]))
|
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mess = "First index of the range must be smaller or equal to the second"
|
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assert i1 <= i2, mess
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ion_list = np.array(range(i1 - 1, i2))
|
||||
else:
|
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# Check if a set of indices is given
|
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try:
|
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l_tmp = map(int, par_str.split())
|
||||
l_tmp.sort()
|
||||
# Subtract 1 so that VASP indices (starting with 1) are converted
|
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# to Python indices (starting with 0)
|
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ion_list = np.array(l_tmp) - 1
|
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@ -89,6 +108,9 @@ class ConfigParameters:
|
||||
err_msg = "Only an option with a list of ion indices is implemented"
|
||||
raise NotImplementedError(err_msg)
|
||||
|
||||
err_mess = "Lowest ion index is smaller than 1 in '%s'"%(par_str)
|
||||
assert np.all(ion_list >= 0), err_mess
|
||||
|
||||
return ion_list
|
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|
||||
################################################################################
|
||||
@ -102,8 +124,44 @@ class ConfigParameters:
|
||||
(case does not matter). In fact, only the first symbol matters so that
|
||||
one can write 'T' or 'F'.
|
||||
"""
|
||||
assert par_str[0] in 'tf', "Logical parameters should be given by either 'True' or 'False'"
|
||||
return par_str[0] == 't'
|
||||
first_char = par_str[0].lower()
|
||||
assert first_char in 'tf', "Logical parameters should be given by either 'True' or 'False'"
|
||||
return first_char == 't'
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# parse_string_tmatrix()
|
||||
#
|
||||
################################################################################
|
||||
def parse_string_tmatrix(self, par_str, real):
|
||||
"""
|
||||
Transformation matrix is defined as a set of rows separated
|
||||
by a new line symbol.
|
||||
"""
|
||||
str_rows = par_str.split('\n')
|
||||
try:
|
||||
rows = [map(float, s.split()) for s in str_rows]
|
||||
except ValueError:
|
||||
err_mess = "Cannot parse a matrix string:\n%s"%(par_str)
|
||||
raise ValueError(err_mess)
|
||||
|
||||
nr = len(rows)
|
||||
nm = len(rows[0])
|
||||
|
||||
err_mess = "Number of columns must be the same:\n%s"%(par_str)
|
||||
for row in rows:
|
||||
assert len(row) == nm, err_mess
|
||||
|
||||
if real:
|
||||
mat = np.array(rows)
|
||||
else:
|
||||
err_mess = "Complex matrix must contain 2*M values:\n%s"%(par_str)
|
||||
assert 2 * (nm / 2) == nm, err_mess
|
||||
|
||||
tmp = np.array(rows, dtype=np.complex128)
|
||||
mat = tmp[:, 0::2] + 1.0j * tmp[:, 1::2]
|
||||
|
||||
return mat
|
||||
|
||||
################################################################################
|
||||
#
|
||||
@ -122,7 +180,7 @@ class ConfigParameters:
|
||||
except ConfigParser.NoOptionError:
|
||||
if exception:
|
||||
message = "Required parameter '%s' not found in section [%s]"%(par, section)
|
||||
raise ConfigParser.NoOptionError(message)
|
||||
raise Exception(message)
|
||||
else:
|
||||
continue
|
||||
|
||||
@ -149,9 +207,8 @@ class ConfigParameters:
|
||||
# (note that ConfigParser transforms all names to lower case)
|
||||
sections = self.cp.sections()
|
||||
|
||||
sh_patt = 'shell *([0-9]*)'
|
||||
ismatch = lambda s: not re.match(sh_patt, s) is None
|
||||
sec_shells = filter(ismatch, sections)
|
||||
sh_patt1 = re.compile('shell +.*', re.IGNORECASE)
|
||||
sec_shells = filter(sh_patt1.match, sections)
|
||||
|
||||
self.nshells = len(sec_shells)
|
||||
assert self.nshells > 0, "No projected shells found in the input file"
|
||||
@ -164,15 +221,17 @@ class ConfigParameters:
|
||||
print " Found 1 projected shell"
|
||||
|
||||
# Get shell indices
|
||||
get_ind = lambda s: int(re.match(sh_patt, s).groups()[0])
|
||||
sh_patt2 = re.compile('shell +([0-9]*)$', re.IGNORECASE)
|
||||
try:
|
||||
get_ind = lambda s: int(sh_patt2.match(s).groups()[0])
|
||||
sh_inds = map(get_ind, sec_shells)
|
||||
except ValueError:
|
||||
except (ValueError, AttributeError):
|
||||
raise ValueError("Failed to extract shell indices from a list: %s"%(sec_shells))
|
||||
|
||||
self.sh_sections = {ind: sec for ind, sec in sh_inds, sec_shells}
|
||||
self.sh_sections = {ind: sec for ind, sec in it.izip(sh_inds, sec_shells)}
|
||||
|
||||
# Check that all indices are unique
|
||||
# In principle redundant because the list of sections will contain only unique names
|
||||
assert len(sh_inds) == len(set(sh_inds)), "There must be no shell with the same index!"
|
||||
|
||||
# Ideally, indices should run from 1 to <nshells>
|
||||
@ -180,7 +239,7 @@ class ConfigParameters:
|
||||
sh_inds.sort()
|
||||
if sh_inds != range(1, len(sh_inds) + 1):
|
||||
issue_warning("Shell indices are not uniform or not starting from 1. "
|
||||
"This might be an indication of a incorrect setup."
|
||||
"This might be an indication of a incorrect setup.")
|
||||
|
||||
# Parse shell parameters
|
||||
self.shells = {}
|
||||
@ -230,9 +289,8 @@ class ConfigParameters:
|
||||
# Find group sections
|
||||
sections = self.cp.sections()
|
||||
|
||||
gr_patt = 'group *([0-9]*)'
|
||||
ismatch = lambda s: not re.match(gr_patt, s) is None
|
||||
sec_groups = filter(ismatch, sections)
|
||||
gr_patt = re.compile('group *([0-9]*)')
|
||||
sec_groups = filter(gr_patt.match, sections)
|
||||
|
||||
self.ngroups = len(sec_groups)
|
||||
|
||||
@ -1,13 +0,0 @@
|
||||
[General]
|
||||
|
||||
[PLO Group 1]
|
||||
|
||||
IONS = 5 6 7 8
|
||||
#IONS = Ni
|
||||
EMIN = -0.6
|
||||
EMAX = 2.7
|
||||
LSHELL = 2
|
||||
RTRANSFORM =
|
||||
0.0 0.0 0.0 0.0 1.0
|
||||
0.0 0.0 1.0 0.0 0.0
|
||||
|
||||
20
python/converters/vasp/test/adv_example.cfg
Normal file
20
python/converters/vasp/test/adv_example.cfg
Normal file
@ -0,0 +1,20 @@
|
||||
[General]
|
||||
EFERMI = -0.6
|
||||
|
||||
[Group 1]
|
||||
SHELLS = 1 2
|
||||
EMIN = -7.6
|
||||
EMAX = 2.7
|
||||
|
||||
[Shell 1]
|
||||
# Ni shell
|
||||
IONS = 5 6 7 8
|
||||
LSHELL = 2
|
||||
RTRANSFORM =
|
||||
0.0 0.0 0.0 0.0 1.0
|
||||
0.0 0.0 1.0 0.0 0.0
|
||||
|
||||
[Shell 2]
|
||||
# Oxygen shell
|
||||
IONS = 9..20
|
||||
LSHELL = 1
|
||||
1
python/converters/vasp/test/inpconf/.gitignore
vendored
Normal file
1
python/converters/vasp/test/inpconf/.gitignore
vendored
Normal file
@ -0,0 +1 @@
|
||||
*.pyc
|
||||
1
python/converters/vasp/test/inpconf/runtest.sh
Normal file
1
python/converters/vasp/test/inpconf/runtest.sh
Normal file
@ -0,0 +1 @@
|
||||
PYTHONPATH=../../python:../../c:$PYTHONPATH python $1
|
||||
12
python/converters/vasp/test/inpconf/test1.cfg
Normal file
12
python/converters/vasp/test/inpconf/test1.cfg
Normal file
@ -0,0 +1,12 @@
|
||||
[General]
|
||||
EFERMI = 0.7
|
||||
|
||||
[Group 1]
|
||||
SHELLS = 1
|
||||
|
||||
[Shell 1]
|
||||
LSHELL = 2
|
||||
|
||||
[Shell 2]
|
||||
IONS = 9..20
|
||||
LSHELL = 1
|
||||
4
python/converters/vasp/test/inpconf/test2.cfg
Normal file
4
python/converters/vasp/test/inpconf/test2.cfg
Normal file
@ -0,0 +1,4 @@
|
||||
[General]
|
||||
|
||||
[Group 1]
|
||||
|
||||
5
python/converters/vasp/test/inpconf/test3.cfg
Normal file
5
python/converters/vasp/test/inpconf/test3.cfg
Normal file
@ -0,0 +1,5 @@
|
||||
[General]
|
||||
|
||||
[Group 1]
|
||||
|
||||
[Shell x]
|
||||
7
python/converters/vasp/test/inpconf/test4.cfg
Normal file
7
python/converters/vasp/test/inpconf/test4.cfg
Normal file
@ -0,0 +1,7 @@
|
||||
[General]
|
||||
|
||||
[Group 1]
|
||||
|
||||
[Shell 1]
|
||||
LSHELL = 2
|
||||
|
||||
17
python/converters/vasp/test/inpconf/test5.cfg
Normal file
17
python/converters/vasp/test/inpconf/test5.cfg
Normal file
@ -0,0 +1,17 @@
|
||||
[General]
|
||||
|
||||
[Group 1]
|
||||
SHELLS = 1 2
|
||||
|
||||
[Shell 1]
|
||||
LSHELL = 2
|
||||
IONS = 5..8
|
||||
|
||||
[Shell 2]
|
||||
LSHELL = 1
|
||||
IONS = 1..4
|
||||
|
||||
RTRANSFORM = 0.0 1.0 0.0
|
||||
1.0 0.0 0.0
|
||||
0.0 0.0 1.0
|
||||
|
||||
252
python/converters/vasp/test/inpconf/test_inpconf.py
Normal file
252
python/converters/vasp/test/inpconf/test_inpconf.py
Normal file
@ -0,0 +1,252 @@
|
||||
r"""
|
||||
Test suite for module `inpconf.py`.
|
||||
"""
|
||||
|
||||
import unittest
|
||||
import numpy as np
|
||||
from inpconf import ConfigParameters
|
||||
import ConfigParser
|
||||
|
||||
class TestSpecialParsers(unittest.TestCase):
|
||||
"""
|
||||
Tests of special parsers.
|
||||
"""
|
||||
def __init__(self, *args, **kwargs):
|
||||
"""
|
||||
Initializes a custom equality function for comparing numpy arrays.
|
||||
"""
|
||||
super(TestSpecialParsers, self).__init__(*args, **kwargs)
|
||||
self.addTypeEqualityFunc(np.ndarray, self.is_arrays_equal)
|
||||
|
||||
def is_arrays_equal(self, arr1, arr2, msg=None):
|
||||
"""
|
||||
Raises self.failureException is arrays arr1 and arr2
|
||||
are not equal.
|
||||
"""
|
||||
if not np.allclose(arr1, arr2):
|
||||
raise self.failureException(msg)
|
||||
|
||||
def setUp(self):
|
||||
"""
|
||||
"""
|
||||
pass
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# test_parse_string_logical()
|
||||
#
|
||||
################################################################################
|
||||
def test_parse_string_logical(self):
|
||||
"""
|
||||
Function:
|
||||
|
||||
def parse_string_logical(self, par_str)
|
||||
|
||||
Scenarios:
|
||||
|
||||
- **if** par_str == 'True' **return** True
|
||||
- **if** par_str == 'False' **return** False
|
||||
- **if** par_str == '0' **raise** assertion
|
||||
"""
|
||||
conf_pars = ConfigParameters('test1.cfg')
|
||||
|
||||
# Scenario 1
|
||||
res = conf_pars.parse_string_logical('True')
|
||||
self.assertEqual(res, True)
|
||||
|
||||
# Scenario 2
|
||||
res = conf_pars.parse_string_logical('False')
|
||||
self.assertEqual(res, False)
|
||||
|
||||
# Scenario 3
|
||||
with self.assertRaises(AssertionError):
|
||||
conf_pars.parse_string_logical('0')
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# test_parse_string_ion_list()
|
||||
#
|
||||
################################################################################
|
||||
def test_parse_string_ion_list(self):
|
||||
"""
|
||||
Function:
|
||||
|
||||
def parse_string_ion_list(self, par_str)
|
||||
|
||||
Scenarios:
|
||||
|
||||
- **if** par_str == '5 6 7 8' **return** array([4, 5, 6, 7])
|
||||
- **if** par_str == 'Ni' **raise** NotImplementedError
|
||||
- **if** par_str == '0 1' **raise** AssertionError
|
||||
- **if** par_str == '5..8' **return** array([4, 5, 6, 7])
|
||||
- **if** par_str == '8..5' **raise** AssertionError
|
||||
"""
|
||||
conf_pars = ConfigParameters('test1.cfg')
|
||||
|
||||
# Scenario 1
|
||||
expected = np.array([4, 5, 6, 7])
|
||||
res = conf_pars.parse_string_ion_list('5 6 7 8')
|
||||
self.assertEqual(res, expected)
|
||||
|
||||
# Scenario 2
|
||||
with self.assertRaises(NotImplementedError):
|
||||
conf_pars.parse_string_ion_list('Ni')
|
||||
|
||||
# Scenario 3
|
||||
with self.assertRaises(AssertionError):
|
||||
conf_pars.parse_string_ion_list('0 1')
|
||||
|
||||
# Scenario 4
|
||||
res = conf_pars.parse_string_ion_list('5..8')
|
||||
self.assertEqual(res, expected)
|
||||
|
||||
# Scenario 5
|
||||
err_mess = "First index of the range"
|
||||
with self.assertRaisesRegexp(AssertionError, err_mess):
|
||||
conf_pars.parse_string_ion_list('8..5')
|
||||
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# test_parse_string_tmatrix()
|
||||
#
|
||||
################################################################################
|
||||
def test_parse_string_tmatrix(self):
|
||||
"""
|
||||
Function:
|
||||
|
||||
def parse_string_tmatrix(self, par_str)
|
||||
|
||||
Parses a matrix defined as a set of rows in the conf-file.
|
||||
|
||||
Scenarios:
|
||||
|
||||
- **if** number of columns is not the same **raise** AssertionError
|
||||
- **if** complex matrix is read and the number of columns is odd
|
||||
**raise** AssertionError
|
||||
- **if** a correct matrix is given **return** an array
|
||||
|
||||
"""
|
||||
conf_pars = ConfigParameters('test1.cfg')
|
||||
# Scenario 1
|
||||
par_str = "1.0 0.0\n1.0"
|
||||
err_mess = "Number of columns"
|
||||
with self.assertRaisesRegexp(AssertionError, err_mess):
|
||||
conf_pars.parse_string_tmatrix(par_str, real=True)
|
||||
|
||||
# Scenario 2
|
||||
par_str = "1.0 0.0 2.0 1.0 0.0\n0.0 1.0 2.0 3.0 -1.0"
|
||||
err_mess = "Complex matrix must"
|
||||
with self.assertRaisesRegexp(AssertionError, err_mess):
|
||||
conf_pars.parse_string_tmatrix(par_str, real=False)
|
||||
|
||||
# Scenario 3
|
||||
par_str = "1.0 0.0 2.0 -3.0\n0.0 1.0 -1.0 1.0"
|
||||
res = conf_pars.parse_string_tmatrix(par_str, real=False)
|
||||
expected = np.array([[1.0, 2.0 - 3.0j], [1.0j, -1.0 + 1.0j]])
|
||||
self.assertEqual(res, expected)
|
||||
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# test_parse_parameter_set()
|
||||
#
|
||||
################################################################################
|
||||
def test_parse_parameter_set(self):
|
||||
"""
|
||||
Function:
|
||||
|
||||
def parse_parameter_set(self, section, param_set, excpetion=False)
|
||||
|
||||
Scenarios:
|
||||
|
||||
- **if** config-file section [Shell 1] contains 'LSHELL = 2' **and**
|
||||
'lshell' and 'ions' are in `param_set` **return** a dictionary {'lshell': 2}
|
||||
|
||||
- **if** config-file section [Shell 1] contains 'LSHELL = 2' **and**
|
||||
'lshell' and 'ions' are in `param_set` and
|
||||
exception=True **raise** Exception
|
||||
"""
|
||||
conf_pars = ConfigParameters('test1.cfg')
|
||||
param_set = conf_pars.sh_required # contains 'lshell' and 'ions'
|
||||
|
||||
# Scenario 1
|
||||
res = conf_pars.parse_parameter_set('Shell 1', param_set)
|
||||
expected = {'lshell': 2}
|
||||
self.assertDictEqual(res, expected)
|
||||
|
||||
# Scenario 2
|
||||
section = 'Shell 1'
|
||||
err_mess = "Required parameter" # .* in section [%s]"%(section)
|
||||
with self.assertRaisesRegexp(Exception, err_mess):
|
||||
conf_pars.parse_parameter_set(section, param_set, exception=True)
|
||||
|
||||
################################################################################
|
||||
#
|
||||
# test_parse_shells()
|
||||
#
|
||||
################################################################################
|
||||
def test_parse_shells(self):
|
||||
"""
|
||||
Function:
|
||||
|
||||
def parse_shells(self)
|
||||
|
||||
Scenarios:
|
||||
|
||||
- **if** config-file does not contain a valid [Shell] section
|
||||
**raise** AssertionError
|
||||
- **if** a [Shell] section does not contain a valid index
|
||||
**raise** ValueError
|
||||
- **if** a [Shell] section does not contain all required parameters
|
||||
**raise** Exception
|
||||
- **if** two correct [Shell] sections are defined
|
||||
**return** a dictionary of shell parameters
|
||||
"""
|
||||
# Scenario 1
|
||||
conf_pars = ConfigParameters('test2.cfg')
|
||||
err_mess = "No projected shells"
|
||||
with self.assertRaisesRegexp(AssertionError, err_mess):
|
||||
conf_pars.parse_shells()
|
||||
|
||||
# Scenario 2
|
||||
conf_pars = ConfigParameters('test3.cfg')
|
||||
err_mess = "Failed to extract shell indices"
|
||||
with self.assertRaisesRegexp(ValueError, err_mess):
|
||||
conf_pars.parse_shells()
|
||||
|
||||
# Scenario 3
|
||||
conf_pars = ConfigParameters('test4.cfg')
|
||||
err_mess = "Required parameter"
|
||||
with self.assertRaisesRegexp(Exception, err_mess):
|
||||
conf_pars.parse_shells()
|
||||
|
||||
# Scenario 4
|
||||
conf_pars = ConfigParameters('test5.cfg')
|
||||
conf_pars.parse_shells()
|
||||
res = conf_pars.shells
|
||||
expected = {1: {'lshell': 2, 'ion_list': np.array([4, 5, 6, 7])},
|
||||
2: {'lshell': 1, 'ion_list': np.array([0, 1, 2, 3]),
|
||||
'tmatrix': np.array([[ 0., 1., 0.], [ 1., 0., 0.], [ 0., 0., 1.]])}}
|
||||
self.assertSetEqual(set(res.keys()), set(expected.keys()))
|
||||
|
||||
arr = res[1].pop('ion_list')
|
||||
arr_exp = expected[1].pop('ion_list')
|
||||
self.assertEqual(arr, arr_exp)
|
||||
|
||||
arr = res[2].pop('ion_list')
|
||||
arr_exp = expected[2].pop('ion_list')
|
||||
self.assertEqual(arr, arr_exp)
|
||||
|
||||
arr = res[2].pop('tmatrix')
|
||||
arr_exp = expected[2].pop('tmatrix')
|
||||
self.assertEqual(arr, arr_exp)
|
||||
|
||||
self.assertDictEqual(res, expected)
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
suite = unittest.TestLoader().loadTestsFromTestCase(TestSpecialParsers)
|
||||
# unittest.TextTestRunner(verbosity=2, buffer=False).run(suite)
|
||||
unittest.TextTestRunner(verbosity=2, buffer=True).run(suite)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user