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wham2d can now hide some output when verbose is set to False

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Daniel Bauer
2019-07-31 13:10:14 +02:00
parent f25288e4f5
commit 074d399984
2 changed files with 11 additions and 7 deletions
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2
adaptiveumbrella/__init__.py
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@@ -3,4 +3,4 @@ from .runner import UmbrellaRunner
from .wham2d import WHAM2DRunner from .wham2d import WHAM2DRunner
__all__ = ['AdaptiveUmbrella'] __all__ = ['AdaptiveUmbrella']
__version__ = "0.3.5" __version__ = "0.3.6"

16
adaptiveumbrella/wham2d.py
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@@ -21,6 +21,7 @@ class WHAM2DRunner(UmbrellaRunner):
def __init__(self): def __init__(self):
UmbrellaRunner.__init__(self) UmbrellaRunner.__init__(self)
self.verbose = False
self.WHAM_EXEC = 'wham-2d' self.WHAM_EXEC = 'wham-2d'
self.tmp_folder = "tmp/WHAM" self.tmp_folder = "tmp/WHAM"
self.simulation_folder = "tmp/simulations" self.simulation_folder = "tmp/simulations"
@@ -34,7 +35,7 @@ class WHAM2DRunner(UmbrellaRunner):
with open(path, 'w') as out: with open(path, 'w') as out:
for file in os.listdir(self.simulation_folder): for file in os.listdir(self.simulation_folder):
filepath = os.path.join(self.simulation_folder, file, "COLVAR") filepath = os.path.join(self.simulation_folder, file, "COLVAR")
if not os.path.exists(filepath): if not os.path.exists(filepath) and self.verbose:
print("Not found: {}".format(filepath)) print("Not found: {}".format(filepath))
continue continue
prefix, x, y = file.split("_") prefix, x, y = file.split("_")
@@ -59,9 +60,9 @@ class WHAM2DRunner(UmbrellaRunner):
self._get_lambdas_for_index((nonzero[0].min(), nonzero[1].min())), self._get_lambdas_for_index((nonzero[0].min(), nonzero[1].min())),
self._get_lambdas_for_index((nonzero[0].max(), nonzero[1].max())) self._get_lambdas_for_index((nonzero[0].max(), nonzero[1].max()))
]) ])
borders = borders.flatten() borders = borders.flatten()
# increase borders by 1 lambda step from minimal dimensions # increase borders by 1 lambda step from minimal dimensions
borders[0] -= self.cvs[0][2] borders[0] -= self.cvs[0][2]
borders[1] -= self.cvs[1][2] borders[1] -= self.cvs[1][2]
borders[2] += self.cvs[0][2] borders[2] += self.cvs[0][2]
@@ -88,8 +89,12 @@ class WHAM2DRunner(UmbrellaRunner):
metafile=metafile_path, metafile=metafile_path,
outfile=output_path outfile=output_path
) )
print(cmd) if self.verbose:
err_code = subprocess.call(cmd, shell=True) print(cmd)
err_code = subprocess.call(cmd, shell=True)
else:
FNULL = open(os.devnull, 'w')
err_code = subprocess.call(cmd, shell=True, stdout=FNULL)
if err_code != 0: if err_code != 0:
print("wham exited with error code {}".format(err_code)) print("wham exited with error code {}".format(err_code))
exit(1) exit(1)
@@ -118,7 +123,6 @@ class WHAM2DRunner(UmbrellaRunner):
def calculate_new_pmf(self): def calculate_new_pmf(self):
print("Running wham-2d")
metafile_path = self.create_metadata_file() metafile_path = self.create_metadata_file()
wham_pmf_file = self.get_wham_output_file() wham_pmf_file = self.get_wham_output_file()
self.run_wham2d(metafile_path, wham_pmf_file) self.run_wham2d(metafile_path, wham_pmf_file)