ASR corrected examples (#21)

* update convert-to-json.py

* try/except for mc header file that is not included

* Changpeng's ASR corrected example files

* fix pre-commit

* fix tests

* remove black phosphorus

.ci/dev-requirements.txt

@@ -1,5 +1,6 @@
 pre-commit==2.13.0
-pytest==6.1.2
+pytest==6.2.5
+selenium==4.2.0
 pytest-selenium==2.0.1
 prospector==1.2.0
 pylint==2.4.4

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: https://github.com/ambv/black
-  rev: 21.7b0
+  rev: '22.8.0'
   hooks:
   - id: black
 

compute/__init__.py

@@ -17,7 +17,14 @@
 import qe_tools  # mostly to get its version
 from tools_barebone import __version__ as tools_barebone_version
 
-import header
+# Without the try/except, this fails for convert-to-json.py
+try:
+    import header
+except Exception:
+    import traceback
+
+    traceback.print_exc()
+    print("Continuing without Materials Cloud header.")
 
 __version__ = "21.12.0"
 

config.yaml

@@ -43,9 +43,6 @@ data:
   MoS2-MoS2:
     title: "MoS<sub>2</sub>"
     filename: MoS2-MoS2.json
-  P:
-    title: "P"
-    filename: P.json
   PbTe:
     title: "PbTe"
     filename: PbTe.json

convert-to-json.py

@@ -24,20 +24,21 @@
 
 pretty_name_dict = {"BaTiO_3": "BaTiO<sub>3</sub>"}
 
+highsym_qpts_default = [[0, "Γ"], [20, "M"], [40, "K"], [60, "Γ"]]
 highsym_qpts_dict = {
-    "graphene": [[0, "Γ"], [20, "M"], [30, "K"], [50, "Γ"]],
     "BaTiO_3": [[0, "X"], [20, "Γ"], [40, "M"], [60, "Γ"], [100, "R"]],
 }
 
-starting_reps_dict = {"graphene": (5, 5, 1), "BaTiO_3": (3, 3, 3)}
+starting_reps_default = (5, 5, 1)
+starting_reps_dict = {"BaTiO_3": (3, 3, 3)}
 
 
 phonons = QePhononQetools(
     scf_input=scf_input,
     scf_output=scf_output,
     matdyn_modes=matdyn_modes,
-    highsym_qpts=highsym_qpts_dict.get(system_name),
-    starting_reps=starting_reps_dict.get(system_name, (3, 3, 3)),
+    highsym_qpts=highsym_qpts_dict.get(system_name, highsym_qpts_default),
+    starting_reps=starting_reps_dict.get(system_name, starting_reps_default),
     reorder=True,
     name=pretty_name_dict.get(system_name, system_name),
 )

user_static/data/BN/matdyn.frq

@@ -0,0 +1,123 @@
+ &plot nbnd=   6, nks=  61 /
+            0.000000  0.000000  0.000000
+   -0.0004   -0.0000    0.0007  809.5059 1343.4005 1343.4005
+            0.025000  0.014434  0.000000
+    3.5377   43.0165   73.8007  808.4988 1342.6435 1437.6983
+            0.050000  0.028868  0.000000
+   13.5629   86.7308  147.5171  805.6381 1340.4059 1479.5305
+            0.075000  0.043301  0.000000
+   28.4336  131.2616  220.7993  801.3230 1336.7867 1499.5505
+            0.100000  0.057735  0.000000
+   45.8234  176.0063  293.4868  795.9962 1331.9381 1508.8701
+            0.125000  0.072169  0.000000
+   63.3182  219.9002  365.4777  789.9529 1326.0391 1512.5219
+            0.150000  0.086603  0.000000
+   79.1378  261.8108  436.5884  783.2536 1319.2848 1512.6440
+            0.175000  0.101036  0.000000
+   92.7647  300.8991  506.4345  775.7698 1311.8888 1509.8155
+            0.200000  0.115470  0.000000
+  105.1707  336.8663  574.4986  767.3150 1304.0744 1503.9763
+            0.225000  0.129904  0.000000
+  118.3280  369.9087  640.3160  757.7737 1296.0504 1495.0435
+            0.250000  0.144338  0.000000
+  134.0496  400.3815  703.6252  747.1560 1288.0053 1483.1634
+            0.275000  0.158771  0.000000
+  152.9284  428.4211  735.5666  764.3846 1280.1265 1468.6581
+            0.300000  0.173205  0.000000
+  174.2422  453.7985  723.1409  822.6620 1272.6107 1451.8395
+            0.325000  0.187639  0.000000
+  196.6748  476.0868  710.0193  878.4786 1265.6512 1432.8892
+            0.350000  0.202073  0.000000
+  219.0416  494.9649  696.3941  931.7025 1259.4098 1411.8809
+            0.375000  0.216506  0.000000
+  240.5414  510.4252  682.6041  982.0361 1253.9937 1388.9038
+            0.400000  0.230940  0.000000
+  260.5645  522.7469  669.2198 1029.0369 1249.4600 1364.2195
+            0.425000  0.245374  0.000000
+  278.3294  532.2766  657.0714 1072.0117 1245.8447 1338.4686
+            0.450000  0.259808  0.000000
+  292.6610  539.1971  647.1950 1109.5157 1243.1928 1313.1574
+            0.475000  0.274241  0.000000
+  302.1128  543.4607  640.6792 1137.9234 1241.5642 1292.0140
+            0.500000  0.288675  0.000000
+  305.4311  544.9089  638.3942 1149.4065 1241.0137 1282.9426
+            0.491667  0.303109  0.000000
+  305.4016  546.8140  638.2392 1148.8982 1241.1581 1282.4143
+            0.483333  0.317543  0.000000
+  305.3146  552.4626  637.7763 1147.3869 1241.5779 1280.8379
+            0.475000  0.331976  0.000000
+  305.1749  561.6627  637.0113 1144.9114 1242.2347 1278.2395
+            0.466667  0.346410  0.000000
+  304.9907  574.1161  635.9535 1141.5285 1243.0729 1274.6620
+            0.458333  0.360844  0.000000
+  304.7735  589.4483  634.6151 1137.3081 1244.0264 1270.1686
+            0.450000  0.375278  0.000000
+  304.5391  607.2394  633.0107 1132.3262 1245.0164 1264.8515
+            0.441667  0.389711  0.000000
+  304.3083  627.0524  631.1582 1126.6626 1245.9098 1258.8788
+            0.433333  0.404145  0.000000
+  304.1079  629.0792  648.4547 1120.3994 1246.1448 1252.8705
+            0.425000  0.418579  0.000000
+  303.9705  626.8011  671.0321 1113.6240 1242.5388 1250.0906
+            0.416667  0.433013  0.000000
+  303.9341  624.3585  694.3882 1106.4326 1235.3019 1250.4285
+            0.408333  0.447446  0.000000
+  304.0386  621.7953  718.1377 1098.9383 1227.2140 1251.2208
+            0.400000  0.461880  0.000000
+  304.3205  619.1650  741.8867 1091.2811 1218.8226 1252.0461
+            0.391667  0.476314  0.000000
+  304.8055  616.5307  765.2068 1083.6442 1210.3567 1252.8124
+            0.383333  0.490748  0.000000
+  305.5000  613.9645  787.6007 1076.2712 1202.0032 1253.4797
+            0.375000  0.505181  0.000000
+  306.3821  611.5457  808.4686 1069.4819 1193.9506 1254.0257
+            0.366667  0.519615  0.000000
+  307.3953  609.3590  827.0858 1063.6708 1186.4115 1254.4390
+            0.358333  0.534049  0.000000
+  308.4449  607.4932  842.6208 1059.2583 1179.6569 1254.7211
+            0.350000  0.548483  0.000000
+  309.4006  606.0409  854.2381 1056.5458 1174.0632 1254.8857
+            0.341667  0.562917  0.000000
+  310.1030  605.0979  861.3057 1055.4664 1170.1698 1254.9583
+            0.333333  0.577350  0.000000
+  310.3766  604.7619  863.6201 1055.3555 1168.6942 1254.9735
+            0.316667  0.548483  0.000000
+  308.9572  606.2914  855.5196 1053.2007 1175.8289 1255.0073
+            0.300000  0.519615  0.000000
+  304.0701  611.2772  835.0200 1042.8146 1196.9094 1255.4716
+            0.283333  0.490748  0.000000
+  295.3570  619.9946  806.7793 1024.2662 1225.6829 1257.9877
+            0.266667  0.461880  0.000000
+  283.1474  632.1538  773.5032  999.8180 1246.2532 1273.4542
+            0.250000  0.433013  0.000000
+  267.9692  646.9450  736.6055  970.5629 1251.2803 1306.1574
+            0.233333  0.404145  0.000000
+  250.0501  663.2993  696.8567  936.6147 1254.2248 1340.7651
+            0.216667  0.375278  0.000000
+  229.3315  654.7408  680.2040  897.7619 1257.9442 1373.2577
+            0.200000  0.346410  0.000000
+  206.0519  610.6411  696.9200  853.8933 1262.9656 1402.6026
+            0.183333  0.317543  0.000000
+  181.4286  564.9102  713.0217  805.1042 1269.3052 1428.8092
+            0.166667  0.288675  0.000000
+  157.7905  517.8422  728.2755  751.5612 1276.7690 1452.1933
+            0.150000  0.259808  0.000000
+  137.6776  469.5898  693.3367  742.4707 1285.0948 1472.7008
+            0.133333  0.230940  0.000000
+  122.0574  420.1133  630.3896  755.3477 1294.0038 1489.6592
+            0.116667  0.202073  0.000000
+  109.1486  369.2501  562.7113  766.6851 1303.1942 1502.1631
+            0.100000  0.173205  0.000000
+   95.5452  316.9099  490.5109  776.4610 1312.3104 1509.7648
+            0.083333  0.144338  0.000000
+   78.6992  263.2913  414.2991  784.9094 1320.9177 1512.7604
+            0.066667  0.115470  0.000000
+   58.4563  208.9832  334.8263  792.3630 1328.5433 1511.4980
+            0.050000  0.086603  0.000000
+   37.0115  154.8646  252.9333  798.9611 1334.8031 1504.7149
+            0.033333  0.057735  0.000000
+   17.8988  101.7987  169.4120  804.4374 1339.4736 1487.3177
+            0.016667  0.028868  0.000000
+    4.7052   50.2159   84.9266  808.1694 1342.3966 1446.3945
+            0.000000  0.000000  0.000000
+   -0.0004   -0.0000    0.0007  809.5059 1343.4005 1343.4005

user_static/data/BN/matdyn.frq.gp

@@ -0,0 +1,61 @@
+  0.000000      -0.0004   -0.0000    0.0007  809.5059 1343.4005 1343.4005
+  0.028868       3.5377   43.0165   73.8007  808.4988 1342.6435 1437.6983
+  0.057735      13.5629   86.7308  147.5171  805.6381 1340.4059 1479.5305
+  0.086603      28.4336  131.2616  220.7993  801.3230 1336.7867 1499.5505
+  0.115470      45.8234  176.0063  293.4868  795.9962 1331.9381 1508.8701
+  0.144338      63.3182  219.9002  365.4777  789.9529 1326.0391 1512.5219
+  0.173205      79.1378  261.8108  436.5884  783.2536 1319.2848 1512.6440
+  0.202073      92.7647  300.8991  506.4345  775.7698 1311.8888 1509.8155
+  0.230940     105.1707  336.8663  574.4986  767.3150 1304.0744 1503.9763
+  0.259808     118.3280  369.9087  640.3160  757.7737 1296.0504 1495.0435
+  0.288675     134.0496  400.3815  703.6252  747.1560 1288.0053 1483.1634
+  0.317543     152.9284  428.4211  735.5666  764.3846 1280.1265 1468.6581
+  0.346410     174.2422  453.7985  723.1409  822.6620 1272.6107 1451.8395
+  0.375278     196.6748  476.0868  710.0193  878.4786 1265.6512 1432.8892
+  0.404145     219.0416  494.9649  696.3941  931.7025 1259.4098 1411.8809
+  0.433013     240.5414  510.4252  682.6041  982.0361 1253.9937 1388.9038
+  0.461880     260.5645  522.7469  669.2198 1029.0369 1249.4600 1364.2195
+  0.490748     278.3294  532.2766  657.0714 1072.0117 1245.8447 1338.4686
+  0.519615     292.6610  539.1971  647.1950 1109.5157 1243.1928 1313.1574
+  0.548483     302.1128  543.4607  640.6792 1137.9234 1241.5642 1292.0140
+  0.577350     305.4311  544.9089  638.3942 1149.4065 1241.0137 1282.9426
+  0.594017     305.4016  546.8140  638.2392 1148.8982 1241.1581 1282.4143
+  0.610684     305.3146  552.4626  637.7763 1147.3869 1241.5779 1280.8379
+  0.627350     305.1749  561.6627  637.0113 1144.9114 1242.2347 1278.2395
+  0.644017     304.9907  574.1161  635.9535 1141.5285 1243.0729 1274.6620
+  0.660684     304.7735  589.4483  634.6151 1137.3081 1244.0264 1270.1686
+  0.677350     304.5391  607.2394  633.0107 1132.3262 1245.0164 1264.8515
+  0.694017     304.3083  627.0524  631.1582 1126.6626 1245.9098 1258.8788
+  0.710684     304.1079  629.0792  648.4547 1120.3994 1246.1448 1252.8705
+  0.727350     303.9705  626.8011  671.0321 1113.6240 1242.5388 1250.0906
+  0.744017     303.9341  624.3585  694.3882 1106.4326 1235.3019 1250.4285
+  0.760684     304.0386  621.7953  718.1377 1098.9383 1227.2140 1251.2208
+  0.777350     304.3205  619.1650  741.8867 1091.2811 1218.8226 1252.0461
+  0.794017     304.8055  616.5307  765.2068 1083.6442 1210.3567 1252.8124
+  0.810684     305.5000  613.9645  787.6007 1076.2712 1202.0032 1253.4797
+  0.827350     306.3821  611.5457  808.4686 1069.4819 1193.9506 1254.0257
+  0.844017     307.3953  609.3590  827.0858 1063.6708 1186.4115 1254.4390
+  0.860684     308.4449  607.4932  842.6208 1059.2583 1179.6569 1254.7211
+  0.877350     309.4006  606.0409  854.2381 1056.5458 1174.0632 1254.8857
+  0.894017     310.1030  605.0979  861.3057 1055.4664 1170.1698 1254.9583
+  0.910684     310.3766  604.7619  863.6201 1055.3555 1168.6942 1254.9735
+  0.944017     308.9572  606.2914  855.5196 1053.2007 1175.8289 1255.0073
+  0.977350     304.0701  611.2772  835.0200 1042.8146 1196.9094 1255.4716
+  1.010684     295.3570  619.9946  806.7793 1024.2662 1225.6829 1257.9877
+  1.044017     283.1474  632.1538  773.5032  999.8180 1246.2532 1273.4542
+  1.077350     267.9692  646.9450  736.6055  970.5629 1251.2803 1306.1574
+  1.110684     250.0501  663.2993  696.8567  936.6147 1254.2248 1340.7651
+  1.144017     229.3315  654.7408  680.2040  897.7619 1257.9442 1373.2577
+  1.177350     206.0519  610.6411  696.9200  853.8933 1262.9656 1402.6026
+  1.210684     181.4286  564.9102  713.0217  805.1042 1269.3052 1428.8092
+  1.244017     157.7905  517.8422  728.2755  751.5612 1276.7690 1452.1933
+  1.277350     137.6776  469.5898  693.3367  742.4707 1285.0948 1472.7008
+  1.310684     122.0574  420.1133  630.3896  755.3477 1294.0038 1489.6592
+  1.344017     109.1486  369.2501  562.7113  766.6851 1303.1942 1502.1631
+  1.377350      95.5452  316.9099  490.5109  776.4610 1312.3104 1509.7648
+  1.410684      78.6992  263.2913  414.2991  784.9094 1320.9177 1512.7604
+  1.444017      58.4563  208.9832  334.8263  792.3630 1328.5433 1511.4980
+  1.477350      37.0115  154.8646  252.9333  798.9611 1334.8031 1504.7149
+  1.510684      17.8988  101.7987  169.4120  804.4374 1339.4736 1487.3177
+  1.544017       4.7052   50.2159   84.9266  808.1694 1342.3966 1446.3945
+  1.577350      -0.0004   -0.0000    0.0007  809.5059 1343.4005 1343.4005

user_static/data/BN/matdyn.in

@@ -1,9 +1,10 @@
 &INPUT
-asr = 'simple'
+asr = 'all'
+read_lr = .true.
 loto_2d = .true.
 fldos = ''
 flfrc = 'real_space_force_constants.dat'
-flfrq = ''
+flfrq = 'matdyn.frq'
 flvec = 'matdyn.modes'
 q_in_cryst_coord = .true.
 q_in_band_form = .true.