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Merge to mineralscloud/pgm #7

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merged 7 commits into from
Mar 8, 2023
Merged

Merge to mineralscloud/pgm #7

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7a748d7
Merge pull request #2 from MineralsCloud/master
underhill1886 Mar 3, 2023
28e847c
Merge pull request #3 from underhill1886/master
underhill1886 Mar 3, 2023
85f7076
Add unit test for read_input
underhill1886 Mar 5, 2023
76b2794
Test: add unit test for the 2 examples
underhill1886 Mar 5, 2023
8e5c3a3
Fix the S_el value
underhill1886 Mar 8, 2023
cab852a
Modify fe example
underhill1886 Mar 8, 2023
ae17c92
Merge pull request #4 from underhill1886/dev
underhill1886 Mar 8, 2023
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11,946 changes: 5,972 additions & 5,974 deletions examples/fe/data/0K
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11,940 changes: 5,969 additions & 5,971 deletions examples/fe/data/1000K
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11,936 changes: 5,967 additions & 5,969 deletions examples/fe/data/2000K
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11,944 changes: 5,971 additions & 5,973 deletions examples/fe/data/3000K
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11,946 changes: 5,972 additions & 5,974 deletions examples/fe/data/300K
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11,944 changes: 5,971 additions & 5,973 deletions examples/fe/data/4000K
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11,946 changes: 5,972 additions & 5,974 deletions examples/fe/data/5000K
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11,946 changes: 5,972 additions & 5,974 deletions examples/fe/data/6000K
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11,948 changes: 5,973 additions & 5,975 deletions examples/fe/data/7000K
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11,946 changes: 5,972 additions & 5,974 deletions examples/fe/data/8000K
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18 changes: 9 additions & 9 deletions examples/feo/1000K.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Number of volumes(nv), q-vectors(nq), normal mode(np), formula units(nm)
9 264 12 1
P = 1970.3500 V = 158.7365 E = -741.34530945999995 S_el = -0.00000824338000
P = 1970.3500 V = 158.7365 E = -741.34530945999995 S_el = 0.00000824338000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -3433,7 +3433,7 @@ P = 1970.3500 V = 158.7365 E = -741.34530945999995 S_el = -0.00000824338000
771.3486
808.4057
808.4057
P = 2184.9500 V = 155.4939 E = -741.29916915000001 S_el = -0.00000789960000
P = 2184.9500 V = 155.4939 E = -741.29916915000001 S_el = 0.00000789960000
0.0000000 0.0000000 0.0000000
-0.0000
0.0000
Expand Down Expand Up @@ -6866,7 +6866,7 @@ P = 2184.9500 V = 155.4939 E = -741.29916915000001 S_el = -0.00000789960000
796.9645
834.6079
834.6079
P = 2420.1500 V = 152.2585 E = -741.24815776000003 S_el = -0.00000756674000
P = 2420.1500 V = 152.2585 E = -741.24815776000003 S_el = 0.00000756674000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -10299,7 +10299,7 @@ P = 2420.1500 V = 152.2585 E = -741.24815776000003 S_el = -0.00000756674000
821.9341
863.1939
863.1939
P = 2679.1200 V = 149.0177 E = -741.19159462000005 S_el = -0.00000724330000
P = 2679.1200 V = 149.0177 E = -741.19159462000005 S_el = 0.00000724330000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -13732,7 +13732,7 @@ P = 2679.1200 V = 149.0177 E = -741.19159462000005 S_el = -0.00000724330000
849.6428
891.9755
891.9755
P = 2964.1600 V = 145.7779 E = -741.12904962000005 S_el = -0.00000692891000
P = 2964.1600 V = 145.7779 E = -741.12904962000005 S_el = 0.00000692891000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -17165,7 +17165,7 @@ P = 2964.1600 V = 145.7779 E = -741.12904962000005 S_el = -0.00000692891000
874.5631
921.6055
921.6055
P = 3278.4200 V = 142.5364 E = -741.05983870000000 S_el = -0.00000662096000
P = 3278.4200 V = 142.5364 E = -741.05983870000000 S_el = 0.00000662096000
0.0000000 0.0000000 0.0000000
-0.0000
0.0000
Expand Down Expand Up @@ -20598,7 +20598,7 @@ P = 3278.4200 V = 142.5364 E = -741.05983870000000 S_el = -0.00000662096000
904.3898
953.0156
953.0156
P = 3624.8300 V = 139.2993 E = -740.98344099999997 S_el = -0.00000632047000
P = 3624.8300 V = 139.2993 E = -740.98344099999997 S_el = 0.00000632047000
0.0000000 0.0000000 0.0000000
0.0000
0.0000
Expand Down Expand Up @@ -24031,7 +24031,7 @@ P = 3624.8300 V = 139.2993 E = -740.98344099999997 S_el = -0.00000632047000
936.2338
989.1587
989.1587
P = 4008.6800 V = 136.0597 E = -740.89893235000000 S_el = -0.00000603479000
P = 4008.6800 V = 136.0597 E = -740.89893235000000 S_el = 0.00000603479000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -27464,7 +27464,7 @@ P = 4008.6800 V = 136.0597 E = -740.89893235000000 S_el = -0.00000603479000
966.0682
1025.6511
1025.6511
P = 4432.9500 V = 132.8196 E = -740.80550586000004 S_el = -0.00000575366000
P = 4432.9500 V = 132.8196 E = -740.80550586000004 S_el = 0.00000575366000
0.0000000 0.0000000 0.0000000
0.0000
0.0000
Expand Down
18 changes: 9 additions & 9 deletions examples/feo/2000K.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Number of volumes(nv), q-vectors(nq), normal mode(np), formula units(nm)
9 264 12 1
P = 1988.0900 V = 158.7365 E = -741.33423189999996 S_el = -0.00001578686000
P = 1988.0900 V = 158.7365 E = -741.33423189999996 S_el = 0.00001578686000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -3433,7 +3433,7 @@ P = 1988.0900 V = 158.7365 E = -741.33423189999996 S_el = -0.00001578686000
766.4986
807.1948
807.1948
P = 2202.4800 V = 155.4939 E = -741.28840636999996 S_el = -0.00001522033000
P = 2202.4800 V = 155.4939 E = -741.28840636999996 S_el = 0.00001522033000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -6866,7 +6866,7 @@ P = 2202.4800 V = 155.4939 E = -741.28840636999996 S_el = -0.00001522033000
790.7428
833.9326
833.9326
P = 2437.4300 V = 152.2585 E = -741.23771687999999 S_el = -0.00001466171500
P = 2437.4300 V = 152.2585 E = -741.23771687999999 S_el = 0.00001466171500
0.0000000 0.0000000 0.0000000
-0.0000
0.0000
Expand Down Expand Up @@ -10299,7 +10299,7 @@ P = 2437.4300 V = 152.2585 E = -741.23771687999999 S_el = -0.00001466171500
817.2238
860.8953
860.8953
P = 2696.1400 V = 149.0177 E = -741.18148128999997 S_el = -0.00001411073000
P = 2696.1400 V = 149.0177 E = -741.18148128999997 S_el = 0.00001411073000
0.0000000 0.0000000 0.0000000
0.0000
0.0000
Expand Down Expand Up @@ -13732,7 +13732,7 @@ P = 2696.1400 V = 149.0177 E = -741.18148128999997 S_el = -0.00001411073000
843.4678
888.0103
888.0103
P = 2980.9100 V = 145.7779 E = -741.11926472000005 S_el = -0.00001357040500
P = 2980.9100 V = 145.7779 E = -741.11926472000005 S_el = 0.00001357040500
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -17165,7 +17165,7 @@ P = 2980.9100 V = 145.7779 E = -741.11926472000005 S_el = -0.00001357040500
873.1600
918.8247
918.8247
P = 3294.8600 V = 142.5364 E = -741.05037944000003 S_el = -0.00001304041000
P = 3294.8600 V = 142.5364 E = -741.05037944000003 S_el = 0.00001304041000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -20598,7 +20598,7 @@ P = 3294.8600 V = 142.5364 E = -741.05037944000003 S_el = -0.00001304041000
901.4182
951.4946
951.4946
P = 3640.9400 V = 139.2993 E = -740.97430139999994 S_el = -0.00001252361500
P = 3640.9400 V = 139.2993 E = -740.97430139999994 S_el = 0.00001252361500
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -24031,7 +24031,7 @@ P = 3640.9400 V = 139.2993 E = -740.97430139999994 S_el = -0.00001252361500
931.5827
986.8702
986.8702
P = 4024.4500 V = 136.0597 E = -740.89010015999997 S_el = -0.00001203113500
P = 4024.4500 V = 136.0597 E = -740.89010015999997 S_el = 0.00001203113500
0.0000000 0.0000000 0.0000000
-0.0000
0.0000
Expand Down Expand Up @@ -27464,7 +27464,7 @@ P = 4024.4500 V = 136.0597 E = -740.89010015999997 S_el = -0.00001203113500
961.7829
1022.3158
1022.3158
P = 4448.4200 V = 132.8196 E = -740.79697995000004 S_el = -0.00001154469000
P = 4448.4200 V = 132.8196 E = -740.79697995000004 S_el = 0.00001154469000
0.0000000 0.0000000 0.0000000
-0.0000
0.0000
Expand Down
18 changes: 9 additions & 9 deletions examples/feo/3000K.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Number of volumes(nv), q-vectors(nq), normal mode(np), formula units(nm)
9 264 12 1
P = 2013.2100 V = 158.7365 E = -741.31878806999998 S_el = -0.00002194680333
P = 2013.2100 V = 158.7365 E = -741.31878806999998 S_el = 0.00002194680333
0.0000000 0.0000000 0.0000000
-0.0000
0.0000
Expand Down Expand Up @@ -3433,7 +3433,7 @@ P = 2013.2100 V = 158.7365 E = -741.31878806999998 S_el = -0.00002194680333
766.1361
808.0808
808.0808
P = 2227.5700 V = 155.4939 E = -741.27323428000000 S_el = -0.00002127153333
P = 2227.5700 V = 155.4939 E = -741.27323428000000 S_el = 0.00002127153333
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -6866,7 +6866,7 @@ P = 2227.5700 V = 155.4939 E = -741.27323428000000 S_el = -0.00002127153333
787.8490
833.6379
833.6379
P = 2462.4200 V = 152.2585 E = -741.22283476999996 S_el = -0.00002059666667
P = 2462.4200 V = 152.2585 E = -741.22283476999996 S_el = 0.00002059666667
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -10299,7 +10299,7 @@ P = 2462.4200 V = 152.2585 E = -741.22283476999996 S_el = -0.00002059666667
815.4467
859.9125
859.9125
P = 2720.9900 V = 149.0177 E = -741.16691027000002 S_el = -0.00001992079000
P = 2720.9900 V = 149.0177 E = -741.16691027000002 S_el = 0.00001992079000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -13732,7 +13732,7 @@ P = 2720.9900 V = 149.0177 E = -741.16691027000002 S_el = -0.00001992079000
838.7495
887.3163
887.3163
P = 3005.5500 V = 145.7779 E = -741.10502661999999 S_el = -0.00001924668333
P = 3005.5500 V = 145.7779 E = -741.10502661999999 S_el = 0.00001924668333
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -17165,7 +17165,7 @@ P = 3005.5500 V = 145.7779 E = -741.10502661999999 S_el = -0.00001924668333
867.0723
917.6957
917.6957
P = 3319.2700 V = 142.5364 E = -741.03649504999998 S_el = -0.00001857448000
P = 3319.2700 V = 142.5364 E = -741.03649504999998 S_el = 0.00001857448000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -20598,7 +20598,7 @@ P = 3319.2700 V = 142.5364 E = -741.03649504999998 S_el = -0.00001857448000
895.9490
949.2398
949.2398
P = 3665.0400 V = 139.2993 E = -740.96079126999996 S_el = -0.00001790722667
P = 3665.0400 V = 139.2993 E = -740.96079126999996 S_el = 0.00001790722667
0.0000000 0.0000000 0.0000000
-0.0000
0.0000
Expand Down Expand Up @@ -24031,7 +24031,7 @@ P = 3665.0400 V = 139.2993 E = -740.96079126999996 S_el = -0.00001790722667
927.8648
983.7419
983.7419
P = 4048.1700 V = 136.0597 E = -740.87698939999996 S_el = -0.00001725445000
P = 4048.1700 V = 136.0597 E = -740.87698939999996 S_el = 0.00001725445000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -27464,7 +27464,7 @@ P = 4048.1700 V = 136.0597 E = -740.87698939999996 S_el = -0.00001725445000
958.1356
1020.0833
1020.0833
P = 4471.7000 V = 132.8196 E = -740.78428278000001 S_el = -0.00001660196000
P = 4471.7000 V = 132.8196 E = -740.78428278000001 S_el = 0.00001660196000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down
18 changes: 9 additions & 9 deletions examples/feo/4000K.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Number of volumes(nv), q-vectors(nq), normal mode(np), formula units(nm)
9 264 12 1
P = 2044.2200 V = 158.7365 E = -741.29973887999995 S_el = -0.00002737168750
P = 2044.2200 V = 158.7365 E = -741.29973887999995 S_el = 0.00002737168750
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -3433,7 +3433,7 @@ P = 2044.2200 V = 158.7365 E = -741.29973887999995 S_el = -0.00002737168750
764.1072
809.2996
809.2996
P = 2258.6600 V = 155.4939 E = -741.25446326999997 S_el = -0.00002661742750
P = 2258.6600 V = 155.4939 E = -741.25446326999997 S_el = 0.00002661742750
0.0000000 0.0000000 0.0000000
-0.0000
0.0000
Expand Down Expand Up @@ -6866,7 +6866,7 @@ P = 2258.6600 V = 155.4939 E = -741.25446326999997 S_el = -0.00002661742750
788.1637
834.1684
834.1684
P = 2493.5500 V = 152.2585 E = -741.20435365000003 S_el = -0.00002586017250
P = 2493.5500 V = 152.2585 E = -741.20435365000003 S_el = 0.00002586017250
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -10299,7 +10299,7 @@ P = 2493.5500 V = 152.2585 E = -741.20435365000003 S_el = -0.00002586017250
812.6030
861.2971
861.2971
P = 2752.1400 V = 149.0177 E = -741.14873359000001 S_el = -0.00002509769750
P = 2752.1400 V = 149.0177 E = -741.14873359000001 S_el = 0.00002509769750
0.0000000 0.0000000 0.0000000
-0.0000
0.0000
Expand Down Expand Up @@ -13732,7 +13732,7 @@ P = 2752.1400 V = 149.0177 E = -741.14873359000001 S_el = -0.00002509769750
838.7697
890.0380
890.0380
P = 3036.6900 V = 145.7779 E = -741.08717053999999 S_el = -0.00002433230000
P = 3036.6900 V = 145.7779 E = -741.08717053999999 S_el = 0.00002433230000
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -17165,7 +17165,7 @@ P = 3036.6900 V = 145.7779 E = -741.08717053999999 S_el = -0.00002433230000
866.2492
919.1282
919.1282
P = 3350.3300 V = 142.5364 E = -741.01897641000005 S_el = -0.00002356392500
P = 3350.3300 V = 142.5364 E = -741.01897641000005 S_el = 0.00002356392500
0.0000000 0.0000000 0.0000000
-0.0000
0.0000
Expand Down Expand Up @@ -20598,7 +20598,7 @@ P = 3350.3300 V = 142.5364 E = -741.01897641000005 S_el = -0.00002356392500
895.8089
952.0441
952.0441
P = 3695.9700 V = 139.2993 E = -740.94362930000000 S_el = -0.00002279493000
P = 3695.9700 V = 139.2993 E = -740.94362930000000 S_el = 0.00002279493000
0.0000000 0.0000000 0.0000000
0.0000
0.0000
Expand Down Expand Up @@ -24031,7 +24031,7 @@ P = 3695.9700 V = 139.2993 E = -740.94362930000000 S_el = -0.00002279493000
923.6918
985.1830
985.1830
P = 4078.9000 V = 136.0597 E = -740.86022285000001 S_el = -0.00002202926750
P = 4078.9000 V = 136.0597 E = -740.86022285000001 S_el = 0.00002202926750
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down Expand Up @@ -27464,7 +27464,7 @@ P = 4078.9000 V = 136.0597 E = -740.86022285000001 S_el = -0.00002202926750
955.1100
1021.4130
1021.4130
P = 4502.2000 V = 132.8196 E = -740.76792024999997 S_el = -0.00002126136500
P = 4502.2000 V = 132.8196 E = -740.76792024999997 S_el = 0.00002126136500
0.0000000 0.0000000 0.0000000
-0.0000
-0.0000
Expand Down
19 changes: 19 additions & 0 deletions tests/test_pgm_read_input.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
import pytest
from pgm.reader.read_input import Input

settings = [('examples/casio3/%sK.txt', [1500, 2000, 2500, 3000, 3500, 4000]),
('examples/feo/%sK.txt', [0, 1000, 2000, 3000, 4000])]


@pytest.mark.parametrize("input_dir,discrete_temp", [settings[0]])
def test_casio3_example(input_dir, discrete_temp):
input_instance = Input(input_dir, discrete_temp)
assert input_instance.frequencies.shape == (6, 5, 8000, 15)
assert input_instance.frequencies[0, 0, 0, 3] == 279.853100


@pytest.mark.parametrize("input_dir,discrete_temp", [settings[1]])
def test_feo_example(input_dir, discrete_temp):
input_instance = Input(input_dir, discrete_temp)
assert input_instance.frequencies.shape == (5, 9, 264, 12)
assert input_instance.frequencies[4, 0, 0, 3] == 302.3405
26 changes: 26 additions & 0 deletions tests/test_pgm_runner.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
import pytest
from click.testing import CliRunner
from pgm.cli.main import main

settings = [('examples/casio3/', 'casio3.yaml'), ('examples/feo/', 'feo.yaml')]


@pytest.fixture
def cli_runner():
return CliRunner()


@pytest.mark.parametrize("working_dir, yaml_file", [settings[0]])
def test_casio3_example(cli_runner, working_dir, yaml_file, monkeypatch):
monkeypatch.chdir(working_dir)
result = cli_runner.invoke(main, [yaml_file], prog_name="pgm")
assert result.exit_code == 0
monkeypatch.undo()


@pytest.mark.parametrize("working_dir, yaml_file", [settings[1]])
def test_feo_example(cli_runner, working_dir, yaml_file, monkeypatch):
monkeypatch.chdir(working_dir)
result = cli_runner.invoke(main, [yaml_file], prog_name="pgm")
assert result.exit_code == 0
monkeypatch.undo()