# | Line 3 | Line 3 | import subprocess | |
---|---|---|
3 | import logging | |
4 | import os | |
5 | import subprocess | |
6 | + | import logging |
7 | ||
8 | fraw_list = []#List of all .md files found (even the includes). | |
9 | fmd_list = []#List of all config .md files that can be run (not the includes). | |
# | Line 12 | Line 13 | dir_base = ""#Directory where the script is run from. | |
13 | dir_openmd = ""#Absolute path for openmd | |
14 | dir_base = ""#Directory where the script is run from. | |
15 | ||
16 | + | FORMAT = '%(asctime)-15s %(message)s' |
17 | + | logging.basicConfig(format=FORMAT) |
18 | + | |
19 | """ | |
20 | Function sets up the dir_base and dir_openmd. If an openmd executable is not | |
21 | found, script exits. Function looks for the openmd in the relative location | |
# | Line 20 | Line 24 | def setupDirectories(): | |
24 | """ | |
25 | def setupDirectories(): | |
26 | global dir_base, dir_openmd, dir_cwd | |
27 | + | logger = logging.getLogger("tcpserver") |
28 | dir_base = os.getcwd() | |
29 | if(os.path.isfile("../build/bin/openmd")): | |
30 | os.chdir("../build/bin/") | |
31 | dir_openmd = os.getcwd() | |
32 | os.chdir(dir_base) | |
33 | + | elif(os.path.isfile("../bin/openmd")): |
34 | + | os.chdir("../bin/") |
35 | + | dir_openmd = os.getcwd() |
36 | + | os.chdir(dir_base) |
37 | else: | |
38 | < | print "OpenMD executable not found." |
38 | > | logger.error("OpenMD : %s", "openmd executable not found at the expected location. Script Will Quit...") |
39 | sys.exit() | |
40 | + | forcefld_path = os.path.abspath("../forceFields") |
41 | + | os.environ["FORCE_PARAM_PATH"] = forcefld_path |
42 | ||
32 | – | |
43 | """ | |
44 | Function checks if the sample_file and validate_file (.md files) have the same | |
45 | statusTime = interval time for the stats file. | |
# | Line 45 | Line 55 | def validate_md_time(sample_file, validate_file): | |
55 | validate_status_time = 0 | |
56 | validate_sample_time = 0 | |
57 | validate_run_time = 0 | |
58 | < | |
58 | > | logger = logging.getLogger("tcpserver") |
59 | > | |
60 | samplefh = open(sample_file, "r") | |
61 | validatefh = open(validate_file, "r") | |
62 | ||
# | Line 86 | Line 97 | def validate_md_time(sample_file, validate_file): | |
97 | if (sample_status_time > 0) or (validate_status_time > 0): | |
98 | if sample_status_time == validate_status_time: | |
99 | return True | |
89 | – | else: |
90 | – | return False |
100 | ||
101 | if (sample_sample_time > 0) or (validate_sample_time > 0): | |
102 | if sample_sample_time == validate_sample_time: | |
103 | return True | |
95 | – | else: |
96 | – | return False |
104 | ||
105 | if (sample_run_time > 0) or (validate_run_time > 0): | |
106 | if sample_run_time == validate_run_time: | |
107 | return True | |
101 | – | else: |
102 | – | return False |
108 | ||
109 | + | logger.warning("MD File: %s", "Sample/Validation times do not match.") |
110 | return False | |
111 | ||
112 | """ | |
# | Line 143 | Line 149 | def compare(fExpected, fNew, epsilon = 0.00001, ignore | |
149 | @return boolean | |
150 | """ | |
151 | def compare(fExpected, fNew, epsilon = 0.00001, ignore_sign=False): | |
152 | + | logger = logging.getLogger("tcpserver") |
153 | fone = open(fExpected, 'r') | |
154 | ftwo = open(fNew, 'r') | |
155 | ||
# | Line 162 | Line 169 | def compare(fExpected, fNew, epsilon = 0.00001, ignore | |
169 | ||
170 | if lenone != lentwo: | |
171 | diffs = diffs + 1 | |
172 | < | print "Line " + str(i) + " do not match in the files." |
172 | > | logger.warning("Line: %d - %s", i, "no mach") |
173 | return True | |
174 | else: | |
175 | for j in range(lenone): | |
# | Line 219 | Line 226 | def runMdFiles(): | |
226 | @author Samuel Njoroge | |
227 | """ | |
228 | def runMdFiles(): | |
229 | + | logger = logging.getLogger("tcpserver") |
230 | global dir_base, dir_openmd, dir_cwd | |
231 | output = [] | |
232 | for x in range(0, len(fmd_list)): | |
233 | #subprocess.call(["export FORCE_PARAM_PATH=/Users/snjoroge/Documents/openmd/development/forceFields"]) | |
234 | if "argon" in fmd_list[x]: | |
235 | < | print "Switching to Directory: " + os.path.dirname(fmd_list[x]) |
235 | > | logger.debug("Switching to Directory: %s", os.path.dirname(fmd_list[x])) |
236 | os.chdir(os.path.dirname(fmd_list[x])) | |
237 | < | print "Running file: " + fmd_list[x] |
237 | > | logger.debug("Running: %s", fmd_list[x]) |
238 | output = subprocess.call([dir_openmd + "/openmd", fmd_list[x]]) | |
239 | if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat")): | |
240 | #print "Renaming File: " + fmd_base_list[x] + ".stat - " + fmd_base_list[x] + "_v.stat" | |
241 | #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"]) | |
242 | < | print "Comparing: " + fmd_base_list[x] + ".stat <=> " + fmd_base_list[x] + "_v.stat" |
242 | > | logger.debug("Comparing: %s", "Comparing: " + fmd_base_list[x] + ".stat <=> " + fmd_base_list[x] + "_v.stat") |
243 | 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")): | |
244 | < | print "Files Do not match." |
244 | > | logger.warning("Files: %s", "Files do not match.") |
245 | else: | |
246 | < | print "Files match." |
246 | > | logger.debug("Files Match") |
247 | os.chdir(dir_base) | |
248 | ||
249 | def cleanUp(): | |
250 | < | print "delete all files generated so not to commit" |
250 | > | print "Delete all files generated." |
251 | for x in range(0, len(fmd_list)): | |
252 | < | print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor" |
253 | < | os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor") |
254 | < | print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat" |
255 | < | os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat") |
256 | < | print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump" |
257 | < | os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump") |
252 | > | if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor")): |
253 | > | print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor" |
254 | > | os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".eor") |
255 | > | if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat")): |
256 | > | print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat" |
257 | > | os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".stat") |
258 | > | if(os.path.exists(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump")): |
259 | > | print "DELETE:" + os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump" |
260 | > | os.remove(os.path.dirname(fmd_list[x]) + "/" + fmd_base_list[x] + ".dump") |
261 |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |