Merge pull request #73 from robinzyb/devel

fix the bug for parsing stresses and forces from restart md output
robinzyb · Aug 26, 2024 · 5688fd7 · 5688fd7
2 parents f6b70d2 + 10c6ebf
commit 5688fd7
Show file tree

Hide file tree

Showing 18 changed files with 2,153 additions and 14 deletions.
diff --git a/cp2kdata/block_parser/header_info.py b/cp2kdata/block_parser/header_info.py
@@ -2,7 +2,9 @@
 from dataclasses import dataclass
 # use monty.re because it can terminate on match
 from monty.re import regrep
+from cp2kdata.log import get_logger
 
+logger = get_logger(__name__)
 
 @dataclass
 class Cp2kInfo:
@@ -43,6 +45,8 @@ def parse_cp2k_info(filename) -> Cp2kInfo:
         raise ValueError(f"More than one restart information found in {filename}")
     elif num_match_restart == 1:
         cp2k_restart = True
+        logger.debug(f"Found restart information in the output header")
+
     elif num_match_restart == 0:
         cp2k_restart = False
 

diff --git a/cp2kdata/output.py b/cp2kdata/output.py
@@ -99,6 +99,7 @@ def __init__(
         # restart should be true or false
         if restart is not None:
             self.cp2k_info.restart = restart
+            logger.debug("Overwrite restart information with user provided restart = True.")
 
         self.check_run_type(run_type=self.global_info.run_type)
 
@@ -401,8 +402,12 @@ def parse_md(self):
             format_logger(info="Forces", filename=self.filename)
             self.atomic_forces_list = parse_atomic_forces_list(
                 self.output_file)
+
+            self.atomic_forces_list = self.drop_first_info(
+                self.cp2k_info, self.atomic_forces_list, info="forces")
+
             self.atomic_forces_list = self.drop_last_info(
-                self.cp2k_info, self.atomic_forces_list)
+                self.cp2k_info, self.atomic_forces_list, info="forces")
 
         stress_file_list = glob.glob(
             os.path.join(self.path_prefix, "*.stress"))
@@ -421,8 +426,13 @@ def parse_md(self):
             self.stress_tensor_list = parse_stress_tensor_list(
                 self.output_file)
 
-            self.stress_tensor_list = self.drop_last_info(
-                self.cp2k_info, self.stress_tensor_list)
+            # stress tensor could be None if the output file doesn't contain stress information
+            if self.stress_tensor_list is not None:
+                self.stress_tensor_list = self.drop_first_info(
+                    self.cp2k_info, self.stress_tensor_list, info="stresses")
+
+                self.stress_tensor_list = self.drop_last_info(
+                    self.cp2k_info, self.stress_tensor_list, info="stresses")
 
         self.num_frames = len(self.energies_list)
 
@@ -521,11 +531,21 @@ def get_vib_freq_list(self):
         return self.vib_freq_list
 
     @staticmethod
-    def drop_last_info(cp2k_info, array):
+    def drop_first_info(cp2k_info, array, info="info"):
+        # drop first info parsed from output if it restart from preivous MD run
+        if cp2k_info.restart == True:
+            logger.info(
+                f"The cp2k output is restarted from previous MD run, drop the first {info}."
+            )
+            array = array[1:]
+        return array
+
+    @staticmethod
+    def drop_last_info(cp2k_info, array, info="info"):
         # drop last info parsed from output if it is terminated by request (touch EXIT)
         if cp2k_info.terminated_by_request == True:
             print(
-                "cp2kdata found the cp2k output is terminated by request, drop the last info.")
+                f"The cp2k output is terminated by user request, drop the last {info}.")
             array = array[:-1]
         return array
 

diff --git a/cp2kdata/utils.py b/cp2kdata/utils.py
@@ -78,14 +78,6 @@ def get_rdf(pos, r, nbin, frames, elements):
         tot_gr += s_gr/frames
     return tot_gr
 
-
-def printtbox(arg):
-    """
-    This function is a print decorated with a few characters so that the
-    print function present a characteristic string. Useful for postprocess.
-    """
-    print("--> CP2KDATA: {0}".format(arg))
-
 def format_logger(info, filename):
     logger.debug(f"Parsing {info:10} from {filename}")
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -10,7 +10,7 @@ name = "Cp2kData"
 version = "0.7.1"
 description = "A Small Package to Postprocess Cp2k Output"
 authors = [
-    {name = "Yongbin Zhuang", email = "[email protected]"}
+    {name = "Yong-Bin Zhuang", email = "[email protected]"}
     ]
 license = {file = "LICENSE"}
 readme = "README.md"

diff --git a/tests/test_dpdata/test_labeledsys.py b/tests/test_dpdata/test_labeledsys.py
@@ -23,6 +23,7 @@
     "tests/test_dpdata/v2022.2/aimd_npt_i",
     "tests/test_dpdata/v2023.1/aimd_nvt",
     "tests/test_dpdata/v2023.1/aimd_npt_f",
+    "tests/test_dpdata/v2023.2/aimd_nvt_restart",
     "tests/test_dpdata/v2024.1/aimd_npt_i_restart"
 ]
 

diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/H2O_restart-1.cell b/tests/test_dpdata/v2023.2/aimd_nvt_restart/H2O_restart-1.cell
@@ -0,0 +1,4 @@
+#   Step   Time [fs]       Ax [Angstrom]       Ay [Angstrom]       Az [Angstrom]       Bx [Angstrom]       By [Angstrom]       Bz [Angstrom]       Cx [Angstrom]       Cy [Angstrom]       Cz [Angstrom]      Volume [Angstrom^3]
+      20      20.000       12.6000000000        0.0000000000        0.0000000000        0.0000000000       12.6000000000        0.0000000000        0.0000000000        0.0000000000       12.6000000000          2000.3760000000
+      21      21.000       12.6000000000        0.0000000000        0.0000000000        0.0000000000       12.6000000000        0.0000000000        0.0000000000        0.0000000000       12.6000000000          2000.3760000000
+      22      22.000       12.6000000000        0.0000000000        0.0000000000        0.0000000000       12.6000000000        0.0000000000        0.0000000000        0.0000000000       12.6000000000          2000.3760000000
diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/H2O_restart-1.ener b/tests/test_dpdata/v2023.2/aimd_nvt_restart/H2O_restart-1.ener
@@ -0,0 +1,4 @@
+#     Step Nr.          Time[fs]        Kin.[a.u.]          Temp[K]            Pot.[a.u.]        Cons Qty[a.u.]        UsedTime[s]
+        20           20.000000         0.023548744       413.116461989       -68.977821523       -68.938997773        60.277769099
+        21           21.000000         0.021234705       372.521196861       -68.975543745       -68.938783638        18.870602752
+        22           22.000000         0.018025570       316.223219413       -68.972324812       -68.938309176        18.600492027
diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/H2O_restart-frc-1.xyz b/tests/test_dpdata/v2023.2/aimd_nvt_restart/H2O_restart-frc-1.xyz
@@ -0,0 +1,42 @@
+      12
+ i =       20, time =       20.000, E =       -68.9778215227
+  O         0.0102121326        0.0082450214        0.0258173651
+  H         0.0011582980       -0.0132266233       -0.0121033560
+  H        -0.0123640908        0.0039438113       -0.0130423386
+  O         0.0005078165       -0.0022005368        0.0001827544
+  H        -0.0125006144       -0.0143064065       -0.0000614894
+  H         0.0132352169        0.0161774021       -0.0019829286
+  O        -0.0052064897        0.0009704681        0.0071012763
+  H        -0.0087157859        0.0035490175        0.0015360158
+  H         0.0131859471       -0.0043854925       -0.0089008239
+  O         0.0295545283        0.0081232015        0.0398825263
+  H        -0.0149641237       -0.0001739602       -0.0009636305
+  H        -0.0147979999       -0.0081434238       -0.0401153032
+      12
+ i =       21, time =       21.000, E =       -68.9755437453
+  O         0.0303052317       -0.0065731816        0.0424437305
+  H        -0.0016013990       -0.0009275749       -0.0040939960
+  H        -0.0304565436        0.0059723068       -0.0378698251
+  O         0.0050859703       -0.0130343569        0.0220011662
+  H        -0.0042172351        0.0055661721       -0.0139265178
+  H        -0.0007481943        0.0074111628       -0.0098332246
+  O         0.0001483569       -0.0013082448        0.0424492183
+  H         0.0060439705       -0.0026121984       -0.0341943831
+  H        -0.0069766144        0.0034709851       -0.0085099322
+  O         0.0025323271        0.0101493554        0.0437780376
+  H         0.0141092427       -0.0024741181       -0.0030324709
+  H        -0.0168895666       -0.0075244283       -0.0421495104
+      12
+ i =       22, time =       22.000, E =       -68.9723248123
+  O         0.0335055352       -0.0223836483        0.0346104595
+  H        -0.0046719265        0.0143965413        0.0055441867
+  H        -0.0306213401        0.0065952030       -0.0402792055
+  O         0.0091840210       -0.0181660032        0.0410637382
+  H         0.0043256547        0.0212885655       -0.0252439822
+  H        -0.0144456375       -0.0028994354       -0.0176576872
+  O         0.0137783287       -0.0069222516        0.0597275234
+  H         0.0149959476       -0.0060552771       -0.0511823329
+  H        -0.0296067618        0.0121169616       -0.0088047186
+  O        -0.0336290172        0.0063977692        0.0209944277
+  H         0.0395185099       -0.0028786832       -0.0055621115
+  H        -0.0058697372       -0.0028984716       -0.0165854098
diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/H2O_restart-pos-1.xyz b/tests/test_dpdata/v2023.2/aimd_nvt_restart/H2O_restart-pos-1.xyz
@@ -0,0 +1,42 @@
+      12
+ i =       20, time =       20.000, E =       -68.9778215227
+  O         6.3316694013       10.3265616457        7.6782392523
+  H         6.1616125544       11.1315146003        8.2239437014
+  H         5.7430023264       10.3807400784        6.9336632835
+  O         9.1302710853        3.1889367305        0.0923448994
+  H         9.4202654175        3.9665554155       -0.4318636659
+  H         8.3566036625        2.7447792754       -0.3225657198
+  O         8.1855081658        2.3324901533        8.5342295228
+  H         8.5124785846        2.1917043131        7.6300685257
+  H         7.2715408397        2.6874938692        8.5035021945
+  O         5.8384192760        0.7389161185        0.6066193230
+  H         6.8100691672        0.6360080101        0.4930624889
+  H         5.4496269488        0.5871999743       -0.2229783996
+      12
+ i =       21, time =       21.000, E =       -68.9755437453
+  O         6.3293442164       10.3288510035        7.6890530379
+  H         6.1740088133       11.1227075298        8.2233525135
+  H         5.7769852068       10.3802955549        6.9499194570
+  O         9.1250871242        3.1883703779        0.0926188564
+  H         9.4289965462        3.9283149440       -0.4278630874
+  H         8.3858327801        2.7327027774       -0.3239566886
+  O         8.1848476170        2.3295429395        8.5347657971
+  H         8.5165756164        2.1908174768        7.6719777399
+  H         7.2917933703        2.6717934790        8.4917815049
+  O         5.8419706731        0.7321749871        0.5999709745
+  H         6.7859792755        0.6611477233        0.4872188236
+  H         5.4615480885        0.5949492113       -0.2334545867
+      12
+ i =       22, time =       22.000, E =       -68.9723248123
+  O         6.3281856704       10.3305920763        7.7009772804
+  H         6.1843416649       11.1136446689        8.2209119268
+  H         5.7987343252       10.3828672891        6.9478903583
+  O         9.1202725251        3.1873331964        0.0935722685
+  H         9.4378150638        3.8939808908       -0.4307181071
+  H         8.4139336323        2.7247774685       -0.3310485390
+  O         8.1840146377        2.3261956596        8.5367461425
+  H         8.5236234033        2.1884016296        7.6935468334
+  H         7.3114734045        2.6581072367        8.4768182088
+  O         5.8452782009        0.7260571216        0.5950798598
+  H         6.7689899409        0.6869585853        0.4797432756
+  H         5.4641863879        0.5990944245       -0.2660469140
diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/H2O_restart-vel-1.xyz b/tests/test_dpdata/v2023.2/aimd_nvt_restart/H2O_restart-vel-1.xyz
@@ -0,0 +1,42 @@
+      12
+ i =       20, time =       20.000, E =       -68.9778215227
+  O        -0.0001207346        0.0001074056        0.0004703622
+  H         0.0005855913       -0.0002574846        0.0001154687
+  H         0.0015998529       -0.0000622831        0.0008679529
+  O        -0.0002418940       -0.0000233290        0.0000124543
+  H         0.0004797014       -0.0015905338        0.0001841869
+  H         0.0011941590       -0.0007528683       -0.0000373856
+  O        -0.0000234917       -0.0001275842        0.0000186304
+  H         0.0002868016       -0.0000755973        0.0019817826
+  H         0.0007269848       -0.0006756403       -0.0004509122
+  O         0.0001475795       -0.0003198904       -0.0003427299
+  H        -0.0009340985        0.0011038179       -0.0002542683
+  H         0.0007589708        0.0004430338       -0.0000267723
+      12
+ i =       21, time =       21.000, E =       -68.9755437453
+  O        -0.0000795425        0.0000918312        0.0005236683
+  H         0.0005186287       -0.0004079899       -0.0000691496
+  H         0.0012742614        0.0000486147        0.0003249063
+  O        -0.0002286140       -0.0000366232        0.0000280261
+  H         0.0003974182       -0.0016667569        0.0000261553
+  H         0.0013137980       -0.0004568710       -0.0001927501
+  O        -0.0000339289       -0.0001437524        0.0000573246
+  H         0.0002544726       -0.0000749897        0.0014528407
+  H         0.0009090015       -0.0006714956       -0.0006097483
+  O         0.0001568165       -0.0002942565       -0.0002637349
+  H        -0.0009396582        0.0011656603       -0.0003041364
+  H         0.0003321132        0.0002716318       -0.0009836074
+      12
+ i =       22, time =       22.000, E =       -68.9723248123
+  O        -0.0000272789        0.0000584253        0.0005504840
+  H         0.0003970076       -0.0002502477       -0.0000466458
+  H         0.0006807280        0.0001984450       -0.0005602733
+  O        -0.0002087397       -0.0000628053        0.0000727154
+  H         0.0005128035       -0.0012912908       -0.0004154540
+  H         0.0010987018       -0.0003854393       -0.0005791533
+  O        -0.0000317493       -0.0001667080        0.0001405947
+  H         0.0004909749       -0.0001944337        0.0003862865
+  H         0.0006119356       -0.0004846438       -0.0007544230
+  O         0.0001210032       -0.0002674999       -0.0002014346
+  H        -0.0003303746        0.0011846554       -0.0004095307
+  H         0.0000510254        0.0001585657       -0.0017250385
diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/set.000/box.npy b/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/set.000/box.npy
diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/set.000/coord.npy b/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/set.000/coord.npy
diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/set.000/energy.npy b/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/set.000/energy.npy
diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/set.000/force.npy b/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/set.000/force.npy
diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/set.000/virial.npy b/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/set.000/virial.npy
diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/type.raw b/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/type.raw
@@ -0,0 +1,12 @@
+0
+1
+1
+0
+1
+1
+0
+1
+1
+0
+1
+1
diff --git a/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/type_map.raw b/tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/type_map.raw
@@ -0,0 +1,2 @@
+O
+H