fix the bug for parsing stresses and forces from restart md output

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
 

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
 

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}")
 

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 = "robinzhuang@outlook.com"}
+ {name = "Yong-Bin Zhuang", email = "robinzhuang@outlook.com"}
  ]
 license = {file = "LICENSE"}
 readme = "README.md"

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"
 ]
 

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

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

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

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

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

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

tests/test_dpdata/v2023.2/aimd_nvt_restart/deepmd/type_map.raw

@@ -0,0 +1,2 @@
+O
+H