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chuckv |
1659 |
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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chuckv |
1660 |
import logging |
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chuckv |
1659 |
|
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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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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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chuckv |
1660 |
FORMAT = '%(asctime)-15s %(message)s' |
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logging.basicConfig(format=FORMAT) |
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chuckv |
1659 |
""" |
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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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chuckv |
1660 |
logger = logging.getLogger("tcpserver") |
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chuckv |
1659 |
dir_base = os.getcwd() |
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if(os.path.isfile("../build/bin/openmd")): |
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chuckv |
1662 |
dir_openmd = os.path.abspath("../build/bin/openmd") |
| 31 |
chuckv |
1661 |
elif(os.path.isfile("../bin/openmd")): |
| 32 |
chuckv |
1662 |
dir_openmd = os.path.abspath("../bin/openmd") |
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chuckv |
1659 |
else: |
| 34 |
chuckv |
1660 |
logger.error("OpenMD : %s", "openmd executable not found at the expected location. Script Will Quit...") |
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chuckv |
1659 |
sys.exit() |
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chuckv |
1661 |
forcefld_path = os.path.abspath("../forceFields") |
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os.environ["FORCE_PARAM_PATH"] = forcefld_path |
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chuckv |
1659 |
|
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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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chuckv |
1660 |
logger = logging.getLogger("tcpserver") |
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chuckv |
1659 |
samplefh = open(sample_file, "r") |
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validatefh = open(validate_file, "r") |
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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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line = samplefh.readline() |
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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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line = validatefh.readline() |
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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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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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| 101 |
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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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chuckv |
1660 |
logger.warning("MD File: %s", "Sample/Validation times do not match.") |
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chuckv |
1659 |
return False |
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""" |
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Function checks if an .md config file and not an include file. |
| 110 |
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@author Samuel Njoroge |
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@param string file - .md file name |
| 112 |
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@return boolean |
| 113 |
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""" |
| 114 |
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def file_is_md(filename): |
| 115 |
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file_handle = open(filename) |
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line = file_handle.readline() |
| 117 |
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| 118 |
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while line: |
| 119 |
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if "<OpenMD version=" in line: |
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return True |
| 121 |
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line = file_handle.readline() |
| 122 |
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| 123 |
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return False |
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""" |
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Function compares two numbers. |
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@author Samuel Njoroge and (). |
| 128 |
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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) |
| 136 |
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return max(one, two) - min(one, two) |
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| 138 |
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""" |
| 139 |
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Function compares two files. |
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@author Samuel Njoroge and (). |
| 141 |
chuckv |
1662 |
@param string fExpected - name of the validation file. |
| 142 |
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@param string fNew - name of the file to validate. |
| 143 |
chuckv |
1659 |
@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 |
| 146 |
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""" |
| 147 |
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def compare(fExpected, fNew, epsilon = 0.00001, ignore_sign=False): |
| 148 |
chuckv |
1660 |
logger = logging.getLogger("tcpserver") |
| 149 |
chuckv |
1659 |
fone = open(fExpected, 'r') |
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ftwo = open(fNew, 'r') |
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diffs = 0 |
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| 154 |
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i = 0 |
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for lineone in fone: |
| 156 |
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linetwo = ftwo.readline() |
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elementsone = lineone.split() |
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elementstwo = linetwo.split() |
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i = i + 1 |
| 162 |
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lenone = len(elementsone) |
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lentwo = len(elementstwo) |
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if lenone != lentwo: |
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diffs = diffs + 1 |
| 168 |
chuckv |
1660 |
logger.warning("Line: %d - %s", i, "no mach") |
| 169 |
chuckv |
1659 |
return True |
| 170 |
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else: |
| 171 |
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for j in range(lenone): |
| 172 |
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# used to ignore XYZ meta data such as # of frames and # of atoms |
| 173 |
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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 |
| 177 |
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continue |
| 178 |
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except ValueError: |
| 179 |
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pass |
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try: |
| 181 |
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feone = float(elementsone[j]) |
| 182 |
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fetwo = float(elementstwo[j]) |
| 183 |
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| 184 |
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fediff = absDiff(feone, fetwo, ignore_sign) |
| 185 |
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| 186 |
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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." |
| 189 |
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return True |
| 190 |
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except ValueError: |
| 191 |
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pass |
| 192 |
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return False#diffs == 0 |
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| 194 |
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""" |
| 195 |
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Function scans the directory for .md config files which will be run for |
| 196 |
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testing. |
| 197 |
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@author Samuel Njoroge |
| 198 |
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""" |
| 199 |
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def scanForMdFiles(): |
| 200 |
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paths = [] |
| 201 |
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variable = "sam is here" |
| 202 |
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for p in os.listdir("../samples/"): |
| 203 |
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paths.append(os.path.abspath("../samples/" + p)) |
| 204 |
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| 205 |
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while len(paths): |
| 206 |
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p = paths.pop() |
| 207 |
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if os.path.isfile(p): |
| 208 |
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fraw_list.append(p) |
| 209 |
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else: |
| 210 |
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for np in os.listdir(p): |
| 211 |
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paths.append(os.path.abspath(p + "/" + np)) |
| 212 |
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| 213 |
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for f in fraw_list: |
| 214 |
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if (".md" in f) and (not ".svn" in f) and file_is_md(f): |
| 215 |
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fmd_list.append(f) |
| 216 |
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temp = os.path.basename(f) |
| 217 |
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temp = temp.replace(".md",'') |
| 218 |
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fmd_base_list.append(temp) |
| 219 |
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| 220 |
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""" |
| 221 |
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Function runs OpenMD on the files the compares them with the already run files (*_v.stat) |
| 222 |
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@author Samuel Njoroge |
| 223 |
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""" |
| 224 |
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def runMdFiles(): |
| 225 |
chuckv |
1660 |
logger = logging.getLogger("tcpserver") |
| 226 |
chuckv |
1659 |
global dir_base, dir_openmd, dir_cwd |
| 227 |
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output = [] |
| 228 |
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for x in range(0, len(fmd_list)): |
| 229 |
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if "argon" in fmd_list[x]: |
| 230 |
chuckv |
1660 |
logger.debug("Switching to Directory: %s", os.path.dirname(fmd_list[x])) |
| 231 |
chuckv |
1659 |
os.chdir(os.path.dirname(fmd_list[x])) |
| 232 |
chuckv |
1660 |
logger.debug("Running: %s", fmd_list[x]) |
| 233 |
chuckv |
1659 |
output = subprocess.call([dir_openmd + "/openmd", fmd_list[x]]) |
| 234 |
chuckv |
1662 |
if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat") and os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + "_v.stat")): |
| 235 |
chuckv |
1659 |
#print "Renaming File: " + fmd_base_list[x] + ".stat - " + fmd_base_list[x] + "_v.stat" |
| 236 |
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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"]) |
| 237 |
chuckv |
1660 |
logger.debug("Comparing: %s", "Comparing: " + fmd_base_list[x] + ".stat <=> " + fmd_base_list[x] + "_v.stat") |
| 238 |
chuckv |
1659 |
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")): |
| 239 |
chuckv |
1662 |
logger.warning("Files: Files do not match.") |
| 240 |
chuckv |
1659 |
else: |
| 241 |
chuckv |
1660 |
logger.debug("Files Match") |
| 242 |
chuckv |
1662 |
else: |
| 243 |
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logger.warning("Stat Files: one of the files was not found: %s \n %s", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + "_v.stat") |
| 244 |
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| 245 |
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if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor") and os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + "_v.eor")): |
| 246 |
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#print "Renaming File: " + fmd_base_list[x] + ".stat - " + fmd_base_list[x] + "_v.stat" |
| 247 |
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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"]) |
| 248 |
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logger.debug("Comparing: %s", "Comparing: " + fmd_base_list[x] + ".eor <=> " + fmd_base_list[x] + "_v.eor") |
| 249 |
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if(compare(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + "_v.eor")): |
| 250 |
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logger.warning("Files: Files do not match.") |
| 251 |
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else: |
| 252 |
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logger.debug("Files Match") |
| 253 |
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else: |
| 254 |
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logger.warning("Eor Files: one of the files was not found: %s \n %s", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor", os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + "_v.eor") |
| 255 |
chuckv |
1659 |
os.chdir(dir_base) |
| 256 |
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|
| 257 |
|
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def cleanUp(): |
| 258 |
chuckv |
1660 |
print "Delete all files generated." |
| 259 |
chuckv |
1659 |
for x in range(0, len(fmd_list)): |
| 260 |
chuckv |
1660 |
if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor")): |
| 261 |
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print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor" |
| 262 |
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os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor") |
| 263 |
|
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if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat")): |
| 264 |
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print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat" |
| 265 |
|
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os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat") |
| 266 |
|
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if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump")): |
| 267 |
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print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump" |
| 268 |
|
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os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump") |
| 269 |
chuckv |
1662 |
|
| 270 |
|
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""" |
| 271 |
|
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Function compares .eor files. It compares sections <StuntDoubles> for position and section <FrameData> for time. |
| 272 |
|
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@author Samuel Njoroge and Dr. Charles Vardeman |
| 273 |
|
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@param string file_validate - name of the validation file. |
| 274 |
|
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@param string file_validate - name of the file to validate. |
| 275 |
|
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@param float epsilon - Precision of the comparison of the files. |
| 276 |
|
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@param boolean ignore_sign - if sign will be a factor in comparing the digits. |
| 277 |
|
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@return boolean |
| 278 |
|
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""" |
| 279 |
|
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def compareEor(file_validate, file_new, epsilon = 0.00001, ignore_sign=False): |
| 280 |
|
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logger = logging.getLogger("tcpserver") |
| 281 |
|
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handlerv = open(file_validate, 'r')#Validate file handler. |
| 282 |
|
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handlern = open(file_new, 'r')#New file handler. |
| 283 |
chuckv |
1659 |
|
| 284 |
chuckv |
1662 |
#Variables. |
| 285 |
|
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indexv = indexn = 0 |
| 286 |
|
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xv = xn = 0.0 |
| 287 |
|
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yv = yn = 0.0 |
| 288 |
|
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zv = zn = 0.0 |
| 289 |
|
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|
| 290 |
|
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#Read first line. |
| 291 |
|
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linev = handlerv.readline() |
| 292 |
|
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linen = handlern.readline() |
| 293 |
|
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|
| 294 |
|
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while linev: |
| 295 |
|
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if '<StuntDoubles>' in linev: |
| 296 |
|
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linev = handlerv.readline() |
| 297 |
|
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linen = handlern.readline() |
| 298 |
|
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while 2: |
| 299 |
|
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Lv = linev.split() |
| 300 |
|
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Ln = linen.split() |
| 301 |
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|
| 302 |
|
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#If any of these fail, then the files do not match line by line. |
| 303 |
|
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try: |
| 304 |
|
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indexv = int(Lv[0]) |
| 305 |
|
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indexn = int(Ln[0]) |
| 306 |
|
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xv = float(Lv[2]) |
| 307 |
|
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yv = float(Lv[3]) |
| 308 |
|
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zv = float(Lv[4]) |
| 309 |
|
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xn = float(Ln[2]) |
| 310 |
|
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yn = float(Ln[3]) |
| 311 |
|
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zn = float(Ln[4]) |
| 312 |
|
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except: |
| 313 |
|
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logger.warning("Format: files do not follow the same format \n '%s' \n '%s'", linev.strip(), linen.strip()) |
| 314 |
|
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return True |
| 315 |
|
|
|
| 316 |
|
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if indexv != indexn: |
| 317 |
|
|
logger.warning("Indexes do not match: %d | %d", indexv, indexn) |
| 318 |
|
|
|
| 319 |
|
|
fediff = absDiff(xv, xn, ignore_sign) |
| 320 |
|
|
if fediff > epsilon: |
| 321 |
|
|
logger.warning("Line: position x on index %d do not match", indexv) |
| 322 |
|
|
return True |
| 323 |
|
|
|
| 324 |
|
|
fediff = absDiff(yv, yn, ignore_sign) |
| 325 |
|
|
if fediff > epsilon: |
| 326 |
|
|
logger.warning("Line: position y on index %d do not match", indexv) |
| 327 |
|
|
return True |
| 328 |
|
|
|
| 329 |
|
|
fediff = absDiff(zv, zn, ignore_sign) |
| 330 |
|
|
if fediff > epsilon: |
| 331 |
|
|
logger.warning("Line: position z on index %d do not match", indexv) |
| 332 |
|
|
return True |
| 333 |
|
|
|
| 334 |
|
|
linev = handlerv.readline() |
| 335 |
|
|
linen = handlern.readline() |
| 336 |
|
|
|
| 337 |
|
|
if '</StuntDoubles>' in linev: |
| 338 |
|
|
break |
| 339 |
|
|
elif '<FrameData>' in linev: |
| 340 |
|
|
|
| 341 |
|
|
linev = handlerv.readline() |
| 342 |
|
|
linen = handlern.readline() |
| 343 |
|
|
|
| 344 |
|
|
while 1: |
| 345 |
|
|
if 'Time' in linev: |
| 346 |
|
|
Ltv = linev.split(':') |
| 347 |
|
|
Ltn = linen.split(':') |
| 348 |
|
|
|
| 349 |
|
|
if int(Ltv[1]) != int(Ltn[1]): |
| 350 |
|
|
logger.warning("Time: FrameData time does not match.") |
| 351 |
|
|
return True |
| 352 |
|
|
elif '</FrameData>' in linev: |
| 353 |
|
|
break |
| 354 |
|
|
linev = handlerv.readline() |
| 355 |
|
|
linen = handlern.readline() |
| 356 |
|
|
|
| 357 |
|
|
linev = handlerv.readline() |
| 358 |
|
|
linen = handlern.readline() |
| 359 |
|
|
return False |
| 360 |
|
|
|
