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Merge pull request #215 from ICAMS/protect_mv_logs
Protect mv logs
2 parents a85e346 + 49994fc commit 6ed87cb

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8 files changed

+52
-24
lines changed

8 files changed

+52
-24
lines changed

‎.bumpversion.cfg‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
[bumpversion]
2-
current_version = 1.5.6
2+
current_version = 1.5.7
33
commit = True
44
tag = True
55

‎calphy/__init__.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
from calphy.alchemy import Alchemy
55
from calphy.routines import MeltingTemp
66

7-
__version__ = "1.5.6"
7+
__version__ = "1.5.7"
88

99
def addtest(a,b):
1010
return a+b

‎calphy/alchemy.py‎

Lines changed: 12 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -129,8 +129,11 @@ def run_averaging(self):
129129
lmp.close()
130130
# Preserve log file
131131
logfile = os.path.join(self.simfolder, "log.lammps")
132-
if os.path.exists(logfile):
133-
os.rename(logfile, os.path.join(self.simfolder, "averaging.log.lammps"))
132+
try:
133+
if os.path.exists(logfile):
134+
os.rename(logfile, os.path.join(self.simfolder, "averaging.log.lammps"))
135+
except OSError as e:
136+
self.logger.warning(f"Failed to rename log file: {e}")
134137

135138
def run_integration(self, iteration=1):
136139
"""
@@ -475,8 +478,13 @@ def run_integration(self, iteration=1):
475478
lmp.close()
476479
# Preserve log file
477480
logfile = os.path.join(self.simfolder, "log.lammps")
478-
if os.path.exists(logfile):
479-
os.rename(logfile, os.path.join(self.simfolder, "integration.log.lammps"))
481+
try:
482+
if os.path.exists(logfile):
483+
os.rename(
484+
logfile, os.path.join(self.simfolder, "integration.log.lammps")
485+
)
486+
except OSError as e:
487+
self.logger.warning(f"Failed to rename log file: {e}")
480488

481489
def thermodynamic_integration(self):
482490
"""

‎calphy/input.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -49,7 +49,7 @@
4949
from ase.io import read, write
5050
import shutil
5151

52-
__version__ = "1.5.6"
52+
__version__ = "1.5.7"
5353

5454

5555
def _check_equal(val):

‎calphy/liquid.py‎

Lines changed: 9 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -103,8 +103,10 @@ def melt_structure(self, lmp):
103103
lmp.close()
104104
# Preserve log file
105105
logfile = os.path.join(self.simfolder, "log.lammps")
106-
if os.path.exists(logfile):
106+
try:
107107
os.rename(logfile, os.path.join(self.simfolder, "melting.log.lammps"))
108+
except OSError as e:
109+
self.logger.warning(f"Failed to rename log file: {e}")
108110
raise SolidifiedError(
109111
"Liquid system did not melt, maybe try a higher thigh temperature."
110112
)
@@ -182,8 +184,10 @@ def run_averaging(self):
182184
lmp.close()
183185
# Preserve log file
184186
logfile = os.path.join(self.simfolder, "log.lammps")
185-
if os.path.exists(logfile):
187+
try:
186188
os.rename(logfile, os.path.join(self.simfolder, "averaging.log.lammps"))
189+
except OSError as e:
190+
self.logger.warning(f"Failed to rename log file: {e}")
187191

188192
def run_integration(self, iteration=1):
189193
"""
@@ -401,8 +405,10 @@ def run_integration(self, iteration=1):
401405
lmp.close()
402406
# Preserve log file
403407
logfile = os.path.join(self.simfolder, "log.lammps")
404-
if os.path.exists(logfile):
408+
try:
405409
os.rename(logfile, os.path.join(self.simfolder, "integration.log.lammps"))
410+
except OSError as e:
411+
self.logger.warning(f"Failed to rename log file: {e}")
406412

407413
def thermodynamic_integration(self):
408414
"""

‎calphy/phase.py‎

Lines changed: 15 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -281,10 +281,12 @@ def check_if_melted(self, lmp, filename):
281281
lmp.close()
282282
# Preserve log file on error
283283
logfile = os.path.join(self.simfolder, "log.lammps")
284-
if os.path.exists(logfile):
284+
try:
285285
os.rename(
286286
logfile, os.path.join(self.simfolder, "melted_error.log.lammps")
287287
)
288+
except OSError as e:
289+
self.logger.warning(f"Failed to rename log file: {e}")
288290
raise MeltedError(
289291
"System melted, increase size or reduce temp!\n Solid detection algorithm only works with BCC/FCC/HCP/SC/DIA. Detection algorithm can be turned off by setting:\n tolerance.solid_fraction: 0"
290292
)
@@ -296,10 +298,12 @@ def check_if_solidfied(self, lmp, filename):
296298
lmp.close()
297299
# Preserve log file on error
298300
logfile = os.path.join(self.simfolder, "log.lammps")
299-
if os.path.exists(logfile):
301+
try:
300302
os.rename(
301303
logfile, os.path.join(self.simfolder, "solidified_error.log.lammps")
302304
)
305+
except OSError as e:
306+
self.logger.warning(f"Failed to rename log file: {e}")
303307
raise SolidifiedError("System solidified, increase temperature")
304308

305309
def fix_nose_hoover(
@@ -609,13 +613,15 @@ def run_iterative_pressure_convergence(self, lmp):
609613
lmp.close()
610614
# Preserve log file on error
611615
logfile = os.path.join(self.simfolder, "log.lammps")
612-
if os.path.exists(logfile):
616+
try:
613617
os.rename(
614618
logfile,
615619
os.path.join(
616620
self.simfolder, "pressure_convergence_error.log.lammps"
617621
),
618622
)
623+
except OSError as e:
624+
self.logger.warning(f"Failed to rename log file: {e}")
619625
raise ValueError(
620626
"Pressure did not converge after MD runs, maybe change lattice_constant and try?"
621627
)
@@ -732,13 +738,15 @@ def run_iterative_constrained_pressure_convergence(self, lmp):
732738
lmp.close()
733739
# Preserve log file on error
734740
logfile = os.path.join(self.simfolder, "log.lammps")
735-
if os.path.exists(logfile):
741+
try:
736742
os.rename(
737743
logfile,
738744
os.path.join(
739745
self.simfolder, "constrained_pressure_error.log.lammps"
740746
),
741747
)
748+
except OSError as e:
749+
self.logger.warning(f"Failed to rename log file: {e}")
742750
raise ValueError("pressure did not converge")
743751

744752
def process_pressure(
@@ -1333,7 +1341,7 @@ def temperature_scaling(self, iteration=1):
13331341
lmp.command(f"pair_style {self.calc._pair_style_with_options[0]}")
13341342

13351343
# read in conf
1336-
# conf = os.path.join(self.simfolder, "conf.equilibration.dump")
1344+
# conf = os.path.join(self.simfolder, "conf.dump")
13371345
conf = os.path.join(self.simfolder, "conf.equilibration.data")
13381346
lmp = ph.read_data(lmp, conf)
13391347

@@ -1421,12 +1429,12 @@ def temperature_scaling(self, iteration=1):
14211429
lmp.command(
14221430
"fix f2 all npt temp %f %f %f %s %f %f %f"
14231431
% (
1424-
tf,
1432+
t0,
14251433
t0,
14261434
self.calc.md.thermostat_damping[1],
14271435
self.iso,
1428-
pf,
14291436
p0,
1437+
pf,
14301438
self.calc.md.barostat_damping[1],
14311439
)
14321440
)

‎calphy/solid.py‎

Lines changed: 12 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -295,8 +295,11 @@ def run_interactive_averaging(self):
295295
lmp.close()
296296
# Preserve log file
297297
logfile = os.path.join(self.simfolder, "log.lammps")
298-
if os.path.exists(logfile):
299-
os.rename(logfile, os.path.join(self.simfolder, "averaging.log.lammps"))
298+
try:
299+
if os.path.exists(logfile):
300+
os.rename(logfile, os.path.join(self.simfolder, "averaging.log.lammps"))
301+
except OSError as e:
302+
self.logger.warning(f"Failed to rename log file: {e}")
300303

301304
def run_minimal_averaging(self):
302305
"""
@@ -590,10 +593,13 @@ def run_integration(self, iteration=1):
590593
lmp.close()
591594
# Preserve log file
592595
logfile = os.path.join(self.simfolder, "log.lammps")
593-
if os.path.exists(logfile):
594-
os.rename(
595-
logfile, os.path.join(self.simfolder, "integration.log.lammps")
596-
)
596+
try:
597+
if os.path.exists(logfile):
598+
os.rename(
599+
logfile, os.path.join(self.simfolder, "integration.log.lammps")
600+
)
601+
except OSError as e:
602+
self.logger.warning(f"Failed to rename log file: {e}")
597603
else:
598604
file = os.path.join(self.simfolder, "integration.lmp")
599605
lmp.write(file)

‎setup.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -53,7 +53,7 @@
5353
packages=find_packages(include=['calphy', 'calphy.*']),
5454
test_suite='tests',
5555
url='https://github.com/ICAMS/calphy',
56-
version='1.5.6',
56+
version='1.5.7',
5757
zip_safe=False,
5858
entry_points={
5959
'console_scripts': [

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