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import sys |
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import math |
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import logging |
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import os |
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import subprocess |
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import logging |
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|
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fraw_list = []#List of all .md files found (even the includes). |
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fmd_list = []#List of all config .md files that can be run (not the includes). |
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fmd_base_list = []#List of the names of the .md files that can be run. |
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|
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dir_cwd = ""#Current working directory. |
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dir_openmd = ""#Absolute path for openmd |
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dir_base = ""#Directory where the script is run from. |
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|
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FORMAT = '%(asctime)-15s %(message)s' |
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logging.basicConfig(format=FORMAT) |
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|
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""" |
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Function sets up the dir_base and dir_openmd. If an openmd executable is not |
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found, script exits. Function looks for the openmd in the relative location |
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../build/bin but stores the openmd location as an absolute path. |
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@author Samuel Njoroge |
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""" |
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def setupDirectories(): |
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global dir_base, dir_openmd, dir_cwd |
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logger = logging.getLogger("tcpserver") |
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dir_base = os.getcwd() |
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if(os.path.isfile("../build/bin/openmd")): |
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os.chdir("../build/bin/") |
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dir_openmd = os.getcwd() |
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os.chdir(dir_base) |
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elif(os.path.isfile("../bin/openmd")): |
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os.chdir("../bin/") |
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dir_openmd = os.getcwd() |
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os.chdir(dir_base) |
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else: |
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logger.error("OpenMD : %s", "openmd executable not found at the expected location. Script Will Quit...") |
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sys.exit() |
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forcefld_path = os.path.abspath("../forceFields") |
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os.environ["FORCE_PARAM_PATH"] = forcefld_path |
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|
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""" |
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Function checks if the sample_file and validate_file (.md files) have the same |
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statusTime = interval time for the stats file. |
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@author Samuel Njoroge |
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@param string sample_file - .md file that is being run. |
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@param string validate_file - .md file the result is being compared to. |
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@return boolean |
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""" |
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def validate_md_time(sample_file, validate_file): |
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sample_status_time = 0 |
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sample_sample_time = 0 |
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sample_run_time = 0 |
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validate_status_time = 0 |
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validate_sample_time = 0 |
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validate_run_time = 0 |
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logger = logging.getLogger("tcpserver") |
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|
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samplefh = open(sample_file, "r") |
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validatefh = open(validate_file, "r") |
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|
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line = samplefh.readline() |
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while line: |
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if "statusTime" in line: |
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arr = line.split('=') |
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temp = arr[1] |
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sample_status_time = float(temp.replace(';', '')) |
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elif "sampleTime" in line: |
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arr = line.split('=') |
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temp = arr[1] |
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sample_sample_time = float(temp.replace(';', '')) |
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elif "runTime" in line: |
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arr = line.split('=') |
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temp = arr[1] |
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sample_run_time = float(temp.replace(';', '')) |
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|
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line = samplefh.readline() |
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|
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line = validatefh.readline() |
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while line: |
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if "statusTime" in line: |
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arr = line.split('=') |
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temp = arr[1] |
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validate_status_time = float(temp.replace(';', '')) |
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elif "sampleTime" in line: |
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arr = line.split('=') |
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temp = arr[1] |
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validate_sample_time = float(temp.replace(';', '')) |
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elif "runTime" in line: |
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arr = line.split('=') |
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temp = arr[1] |
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validate_run_time = float(temp.replace(';', '')) |
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|
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line = validatefh.readline() |
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|
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if (sample_status_time > 0) or (validate_status_time > 0): |
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if sample_status_time == validate_status_time: |
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return True |
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|
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if (sample_sample_time > 0) or (validate_sample_time > 0): |
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if sample_sample_time == validate_sample_time: |
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return True |
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|
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if (sample_run_time > 0) or (validate_run_time > 0): |
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if sample_run_time == validate_run_time: |
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return True |
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|
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logger.warning("MD File: %s", "Sample/Validation times do not match.") |
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return False |
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|
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""" |
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Function checks if an .md config file and not an include file. |
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@author Samuel Njoroge |
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@param string file - .md file name |
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@return boolean |
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""" |
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def file_is_md(filename): |
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file_handle = open(filename) |
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line = file_handle.readline() |
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|
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while line: |
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if "<OpenMD version=" in line: |
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return True |
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line = file_handle.readline() |
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|
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return False |
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|
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""" |
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Function compares two numbers. |
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@author Samuel Njoroge and (). |
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@param float one - first number to compare. |
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@param float two - second number to compare. |
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@param boolean ignore_sign - if sign is a factor in the comparison. |
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@return float diff - difference between the two numbers. |
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""" |
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def absDiff(one, two, ignore_sign = False): |
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if ignore_sign: |
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one, two = math.fabs(one), math.fabs(two) |
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return max(one, two) - min(one, two) |
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|
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""" |
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Function compares two files. |
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@author Samuel Njoroge and (). |
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@param string fExpected - name of the expected file. |
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@param string fNew - name of the new test file. |
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@param float epsilon - Precision of the comparison of the files. |
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@param boolean ignore_sign - if sign will be a factor in comparing the digits. |
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@return boolean |
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""" |
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def compare(fExpected, fNew, epsilon = 0.00001, ignore_sign=False): |
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logger = logging.getLogger("tcpserver") |
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fone = open(fExpected, 'r') |
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ftwo = open(fNew, 'r') |
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|
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diffs = 0 |
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|
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i = 0 |
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for lineone in fone: |
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linetwo = ftwo.readline() |
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|
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elementsone = lineone.split() |
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elementstwo = linetwo.split() |
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|
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i = i + 1 |
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|
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lenone = len(elementsone) |
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lentwo = len(elementstwo) |
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|
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if lenone != lentwo: |
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diffs = diffs + 1 |
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logger.warning("Line: %d - %s", i, "no mach") |
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return True |
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else: |
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for j in range(lenone): |
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# used to ignore XYZ meta data such as # of frames and # of atoms |
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try: |
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feone = int(elementsone[j]) |
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fetwo = int(elementstwo[j]) |
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# these are ints -- skip this pair |
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continue |
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except ValueError: |
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pass |
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try: |
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feone = float(elementsone[j]) |
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fetwo = float(elementstwo[j]) |
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|
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fediff = absDiff(feone, fetwo, ignore_sign) |
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|
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if fediff > epsilon: |
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diffs = diffs + 1 |
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print "Line " + str(i) + " do not match in the files." |
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return True |
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except ValueError: |
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pass |
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return False#diffs == 0 |
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|
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""" |
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Function scans the directory for .md config files which will be run for |
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testing. |
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@author Samuel Njoroge |
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""" |
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def scanForMdFiles(): |
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paths = [] |
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variable = "sam is here" |
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for p in os.listdir("../samples/"): |
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paths.append(os.path.abspath("../samples/" + p)) |
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|
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while len(paths): |
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p = paths.pop() |
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if os.path.isfile(p): |
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fraw_list.append(p) |
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else: |
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for np in os.listdir(p): |
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paths.append(os.path.abspath(p + "/" + np)) |
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|
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for f in fraw_list: |
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if (".md" in f) and (not ".svn" in f) and file_is_md(f): |
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fmd_list.append(f) |
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temp = os.path.basename(f) |
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temp = temp.replace(".md",'') |
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fmd_base_list.append(temp) |
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|
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""" |
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Function runs OpenMD on the files the compares them with the already run files (*_v.stat) |
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@author Samuel Njoroge |
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""" |
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def runMdFiles(): |
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logger = logging.getLogger("tcpserver") |
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global dir_base, dir_openmd, dir_cwd |
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output = [] |
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for x in range(0, len(fmd_list)): |
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#subprocess.call(["export FORCE_PARAM_PATH=/Users/snjoroge/Documents/openmd/development/forceFields"]) |
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if "argon" in fmd_list[x]: |
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logger.debug("Switching to Directory: %s", os.path.dirname(fmd_list[x])) |
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os.chdir(os.path.dirname(fmd_list[x])) |
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logger.debug("Running: %s", fmd_list[x]) |
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output = subprocess.call([dir_openmd + "/openmd", fmd_list[x]]) |
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if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat")): |
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#print "Renaming File: " + fmd_base_list[x] + ".stat - " + fmd_base_list[x] + "_v.stat" |
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#subprocess.call(["cp", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + "_v.stat"]) |
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logger.debug("Comparing: %s", "Comparing: " + fmd_base_list[x] + ".stat <=> " + fmd_base_list[x] + "_v.stat") |
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if(compare(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + "_v.stat")): |
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logger.warning("Files: %s", "Files do not match.") |
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else: |
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logger.debug("Files Match") |
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os.chdir(dir_base) |
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|
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def cleanUp(): |
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print "Delete all files generated." |
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for x in range(0, len(fmd_list)): |
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if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor")): |
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print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor" |
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os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor") |
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if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat")): |
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print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat" |
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os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat") |
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if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump")): |
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print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump" |
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os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump") |
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|
