def process_serial(binary, input_file):
"""
Runs the apbs binary on a given input file
"""
# First extract the name of the input file's base name
base_name = input_file.split(".")[0]
# The output file should have the same basename
output_name = f"{base_name}.out"
# Ensure that there are sufficient permissions to write to the output file
output_file = open(output_name, "w")
# Construct the system command and make the call
command = [r"{}".format(binary), input_file]
print(f"BINARY: {binary}")
print(f"INPUT: {input_file}")
print(f"COMMAND: {command}")
with subprocess.Popen(
command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
) as proc:
line = str(proc.stdout.read(), "utf-8")
sys.stdout.write(line)
output_file.write(line)
# Look for the results in the output file
output_file = open(output_name, "r")
output_text = output_file.read()
# Look for intermidiate energy results
output_results = check_energies(output_name)
output_pattern = r"Global net (?:ELEC|APOL) energy \= " + FLOAT_PATTERN
output_results2 = [
float(r) for r in re.findall(output_pattern, output_text)
]
output_results += output_results2
# Return all the matched results as a list of floating point numbers
return output_results
def process_serial(binary, input_file):
"""
Runs the apbs binary on a given input file
"""
# First extract the name of the input file's base name
base_name = input_file.split('.')[0]
# The output file should have the same basename
output_name = '%s.out' % base_name
# Ensure that there are sufficient permissions to write to the output file
output_file = open(output_name, 'w')
# Construct the system command and make the call
command = [binary, input_file]
proc = subprocess.Popen(command,
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT)
for line in proc.stdout:
sys.stdout.write(line)
output_file.write(line)
proc.wait()
# Look for the results in the output file
output_file = open(output_name, 'r')
output_text = output_file.read()
# Look for intermidiate energy results
output_results = check_energies(output_name)
output_pattern = r'Global net (?:ELEC|APOL) energy \= ' + float_pattern
output_results2 = [
float(r) for r in re.findall(output_pattern, output_text)
]
output_results += output_results2
# Return all the matched results as a list of floating point numbers
return output_results
def process_serial( binary, input_file ):
"""
Runs the apbs binary on a given input file
"""
# First extract the name of the input file's base name
base_name = input_file.split('.')[0]
# The output file should have the same basename
output_name = '%s.out' % base_name
# Ensure that there are sufficient permissions to write to the output file
output_file = open( output_name, 'w' )
# Construct the system command and make the call
command = [ binary, input_file ]
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
for line in proc.stdout:
sys.stdout.write(line)
output_file.write(line)
proc.wait()
# Look for the results in the output file
output_file = open( output_name, 'r' )
output_text = output_file.read()
# Look for intermidiate energy results
output_results = check_energies(output_name)
output_pattern = r'Global net (?:ELEC|APOL) energy \= ' + float_pattern
output_results2 =[float( r ) for r in re.findall( output_pattern, output_text )]
output_results += output_results2
# Return all the matched results as a list of floating point numbers
return output_results