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Python Pool.temperature方法代码示例

本文整理汇总了Python中ZIBMolPy.pool.Pool.temperature方法的典型用法代码示例。如果您正苦于以下问题:Python Pool.temperature方法的具体用法?Python Pool.temperature怎么用?Python Pool.temperature使用的例子?那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在ZIBMolPy.pool.Pool的用法示例。


在下文中一共展示了Pool.temperature方法的2个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: main

# 需要导入模块: from ZIBMolPy.pool import Pool [as 别名]
# 或者: from ZIBMolPy.pool.Pool import temperature [as 别名]
def main():
    options = options_desc.parse_args(sys.argv)[0]

    if options.common_filename:
        options.molecule = options.common_filename + ".pdb"
        options.presampling = options.common_filename + ".trr"
        options.internals = options.common_filename + ".int"
        options.grompp = options.common_filename + ".mdp"
        options.topology = options.common_filename + ".top"
        options.index = options.common_filename + ".ndx"

    print("Options:\n%s\n" % pformat(eval(str(options))))

    assert path.exists(options.molecule)
    assert path.exists(options.presampling)
    assert path.exists(options.internals)
    assert path.exists(options.grompp)
    assert path.exists(options.topology)

    # TODO: what if there is no index-file? (make_ndx)
    assert path.exists(options.index)
    assert "MOI" in gromacs.read_index_file(options.index), "group MOI should be defined in index file"

    # checks e.g. if the mdp-file looks good
    mdp_options = gromacs.read_mdp_file(options.grompp)

    # options we cannot fix
    for ref_t in re.findall("[0-9]+", mdp_options["ref_t"]):
        assert int(ref_t) == options.temperature, "temperature in mdp file does not match ZIBgridfree temperature"
        # TODO drop options.temperature and get temperature directly from mdp file... ask again if temperature is above 310K

        # options we can fix
    mdp_options_dirty = False  # if set, a new mdp-file will be written
    required_mdp_options = {"dihre": "yes", "dihre_fc": "1", "disre": "simple", "disre_fc": "1"}
    for (k, v) in required_mdp_options.items():
        if mdp_options.has_key(k):
            assert mdp_options[k] == v  # check, if we would overwrite something
        else:
            mdp_options[k] = v
            mdp_options_dirty = True

    if mdp_options.has_key("energygrps"):
        assert "MOI" in [
            str(egrp) for egrp in re.findall("[\S]+", mdp_options["energygrps"])
        ], "group MOI should be among energygrps in mdp file"
    else:
        mdp_options["energygrps"] = "MOI"
        mdp_options_dirty = True

    a, b = mdp_options.has_key("nstxout"), mdp_options.has_key("nstenergy")
    if a and not b:
        mdp_options["nstenergy"] = mdp_options["nstxout"]
        mdp_options_dirty = True
    elif b and not a:
        mdp_options["nstxout"] = mdp_options["nstenergy"]
        mdp_options_dirty = True
    elif b and a:
        assert mdp_options["nstxout"] == mdp_options["nstenergy"], "nstxout should equal nstenergy"

    if int(mdp_options["nsteps"]) > 1e6:
        msg = "Number of MD-steps?"
        mdp_options["nsteps"] = str(userinput(msg, "int", default=int(mdp_options["nsteps"])))

        # create a fixed mdp-file
    if mdp_options_dirty:
        print("Creating copy of mdp-file and adding missing options.")
        out_fn = options.grompp.rsplit(".", 1)[0] + "_fixed.mdp"
        f = open(out_fn, "w")  # append
        f.write("; Generated by zgf_create_pool\n")
        for i in mdp_options.items():
            f.write("%s = %s\n" % i)
        f.write("; EOF\n")
        f.close()
        options.grompp = out_fn

        # check if subsampling is reasonable
    if os.path.getsize(options.presampling) > 100e6:  # 100MB
        print("Presampling trajectory is large")
        trr = TrrFile(options.presampling)
        dt = trr.first_frame.next().t - trr.first_frame.t
        trr.close()
        print("Presampling timestep is %.2f ps" % dt)
        if dt < 10:  # picoseconds
            # TODO: maybe calculate subsampling factor individually, or ask?
            msg = "Subsample presampling trajectory by a tenth?"
            if userinput(msg, "bool"):
                out_fn = options.presampling.rsplit(".", 1)[0] + "_tenth.trr"
                cmd = ["trjconv", "-f", options.presampling, "-o", out_fn, "-skip", "10"]
                check_call(cmd)
                options.presampling = out_fn

                # balance linears
    if options.balance_linears:
        print("Balance Linears")
        old_converter = Converter(options.internals)
        print("Loading presampling....")
        frames = old_converter.read_trajectory(options.presampling)
        new_coord_list = []
        for c in old_converter:
            if not isinstance(c, LinearCoordinate):
#.........这里部分代码省略.........
开发者ID:iwasherefirst2,项目名称:ZIBMolPy,代码行数:103,代码来源:zgf_create_pool.py

示例2: main

# 需要导入模块: from ZIBMolPy.pool import Pool [as 别名]
# 或者: from ZIBMolPy.pool.Pool import temperature [as 别名]
def main():
	options = options_desc.parse_args(sys.argv)[0]

	if(options.common_filename):
		options.molecule = options.common_filename+".pdb"
		options.presampling = options.common_filename+".trr"
		options.internals = options.common_filename+".int"
		options.grompp = options.common_filename+".mdp"
		options.topology = options.common_filename+".top"
		options.index = options.common_filename+".ndx"

	print("Options:\n%s\n"%pformat(eval(str(options))))

	assert(path.exists(options.molecule))
	assert(path.exists(options.presampling))
	assert(path.exists(options.internals))
	assert(path.exists(options.grompp))
	assert(path.exists(options.topology))
		
	#TODO: what if there is no index-file? (make_ndx)
	assert(path.exists(options.index))
	assert('moi' in gromacs.read_index_file(options.index)), "group 'MOI' should be defined in index file"
 
	# checks e.g. if the mdp-file looks good
	mdp_options = gromacs.read_mdp_file(options.grompp)
	
	temperatures = [ref_t for ref_t in re.findall("[0-9]+", mdp_options["ref_t"])]
	assert(len(set(temperatures)) == 1), "temperature definition in mdp file is ambiguous"
	temperature = temperatures[0]

	# get sampling temperature from mdp file
	if(int(temperature) > 310):
		if not(userinput("Your sampling temperature is set to %s K. Continue?"%temperature, "bool")):
			sys.exit("Quit by user.")

	# options we can fix 
 	mdp_options_dirty = False #if set, a new mdp-file will be written

	# the value of the following options need to be fixed
	critical_mdp_options = {"dihre":"yes", "dihre_fc":"1", "disre":"simple", "disre_fc":"1", "gen_temp":temperature}
	for (k,v) in critical_mdp_options.items():
 		if(mdp_options.has_key(k) and mdp_options[k].strip() != v):
			print "Error. I do not want to use '%s' for option '%s' ('%s' required). Please fix your mdp file."%(mdp_options[k].strip(),k,v)
			sys.exit("Quitting.")
 		else:
 			mdp_options[k] = v
 			mdp_options_dirty = True

	# the value of the following options does not matter, but they should be there
	noncritical_mdp_options = {"tcoupl":"no", "pcoupl":"no", "gen_vel":"no", "gen_seed":"-1"}
	for (k,v) in noncritical_mdp_options.items():
		if not(mdp_options.has_key(k)):
			mdp_options[k] = v
			mdp_options_dirty = True

	a = mdp_options.has_key("energygrps") and "moi" not in [str(egrp) for egrp in re.findall('[\S]+', mdp_options["energygrps"])]
	b = not(mdp_options.has_key("energygrps"))
	if(a or b):
		if not(userinput("'MOI' is not defined as an energy group in your mdp file. Maybe you have forgotten to define proper 'energygrps'. Continue?", "bool")):
			sys.exit("Quit by user.")

	a, b = mdp_options.has_key("nstxout"), mdp_options.has_key("nstenergy")
	if(a and not b):
		mdp_options["nstenergy"] = mdp_options["nstxout"]
		mdp_options_dirty = True
	elif(b and not a):
		mdp_options["nstxout"] = mdp_options["nstenergy"]
		mdp_options_dirty = True
	elif(b and a):
		assert(mdp_options["nstxout"] == mdp_options["nstenergy"]), "nstxout should equal nstenergy"
		
	if(int(mdp_options["nsteps"]) > 1e6):
		msg = "Number of MD-steps?"
		mdp_options["nsteps"] = str( userinput(msg, "int", default=int(mdp_options["nsteps"])) )
	
	# create a fixed mdp-file
	if(mdp_options_dirty):
		print("Creating copy of mdp-file and adding missing options.")
		out_fn = options.grompp.rsplit(".", 1)[0] + "_fixed.mdp"
		f = open(out_fn, "w") # append
		f.write("; Generated by zgf_create_pool\n")
		for i in sorted(mdp_options.items()):
			f.write("%s = %s\n"%i)
		f.write("; EOF\n")
		f.close()
		options.grompp = out_fn
		
	
	# check if subsampling is reasonable
	if(os.path.getsize(options.presampling) > 100e6): # 100MB
		print("Presampling trajectory is large")
		trr = TrrFile(options.presampling)
		dt = trr.first_frame.next().t - trr.first_frame.t
		trr.close()
		print("Presampling timestep is %.2f ps"%dt)
		if(dt < 10): # picoseconds
			#TODO: maybe calculate subsampling factor individually, or ask? 
			msg = "Subsample presampling trajectory by a tenth?"
			if(userinput(msg, "bool")):
				out_fn = options.presampling.rsplit(".", 1)[0] + "_tenth.trr"
#.........这里部分代码省略.........
开发者ID:CMD-at-ZIB,项目名称:ZIBMolPy,代码行数:103,代码来源:zgf_create_pool.py


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