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(issue #64) Changes to the python script and the .cfg file are done. …
…As soon as testing is done I'll merge with master.
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kozlac
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Jan 13, 2016
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| #!/usr/bin/env python | ||
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| """ | ||
| Check intermediate computed energies form an APBS run | ||
| """ | ||
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| import sys, re | ||
| from apbs_logger import Logger | ||
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| error_tolerance = 1e-6 | ||
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| class ElecEnergy: | ||
| """ | ||
| extracts and compares computed intermediate energies | ||
| """ | ||
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| pattern = r'\s(?P<label>[a-zA-Z]+ [a-zA-Z]+ = )[\-]?(?P<x>[0-9]+(\.[0-9]+)?(E[\+,\-][0-9]+)?)' | ||
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| def __init__(self, label, x): | ||
| """ | ||
| creates an elecEnergy from supplies values | ||
| """ | ||
| self.label = label | ||
| self.x = x | ||
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| def __init__(self, line): | ||
| """ | ||
| extract energy results from a file at a given line | ||
| """ | ||
| m = re.search(self.pattern, line) | ||
| self.label = m.group('label') | ||
| self.x = float(m.group('x')) | ||
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| def __repr__(self): | ||
| return "ElecEnergy{ label:%S, x:%g" % (self.label, self.x) | ||
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| def diff(self, other): | ||
| """ | ||
| compares the value of two energy calculations | ||
| """ | ||
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| return abs( getattr(self, d) - getattr(other, d) ) | ||
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| def short(self): | ||
| return self.label | ||
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| def extract_energy(energy_class, lines, start_pattern, ): | ||
| """ | ||
| extracts intermediate energies | ||
| """ | ||
| energy_list = [] | ||
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| for line_number, line_text in enumerate(lines): | ||
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| if line_text.lstrip().startswith(start_pattern): | ||
| if re.search(energy_class.pattern, line_text): | ||
| energy_list.append(parse_energy(energy_class, line_text)) | ||
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| return energy_list | ||
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| def parse_energy( energy_class, lines): | ||
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| energy_item = energy_class(lines) | ||
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| return energy_item.x | ||
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| def check_energies(input_file): | ||
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| print "Checking for intermidiate energies in input file %s" % input_file | ||
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| f = None | ||
| try: | ||
| f = open(input_file, 'r') | ||
| except IOError: | ||
| print >> sys.stderr, "Couldn't read from energy file %s" % input_file | ||
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| input_lines = f.readlines() | ||
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| energy_list = extract_energy(ElecEnergy, input_lines, 'Total electrostatic energy') | ||
| energy_list += extract_energy(ElecEnergy, input_lines, 'Mobile charge energy') | ||
| energy_list += extract_energy(ElecEnergy, input_lines, 'Fixed charge energy') | ||
| energy_list += extract_energy(ElecEnergy, input_lines, 'Dielectric energy') | ||
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| return energy_list | ||
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| def test(): | ||
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| l = open('energy.log', 'w') | ||
| logger = Logger(sys.stderr, l) | ||
| energy_list = check_energies('actio_stdout.txt') | ||
| print energy_list | ||
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| if __name__ == '__main__': | ||
| print >> sys.stderr, "The python source files %s is a module and not runnable" % sys.argv[0] | ||
| sys.exit(1) | ||
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