Fixes Player Class Implementation
This commit is contained in:
3
.vscode/settings.json
vendored
3
.vscode/settings.json
vendored
@@ -1,3 +0,0 @@
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{
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"python.pythonPath": "/home/hideyoshi/Python/3.8/bin/python3.8"
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}
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@@ -11,12 +11,13 @@ dice:
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ncores: 3
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nmol: [1, 50]
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dens: 0.75
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nstep: [4000, 6000]
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nstep: [2000, 3000]
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isave: 1000
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ljname: 'phb.ljc'
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outname: 'phb'
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randominit: 'first'
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randominit: 'always'
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gaussian:
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qmprog: 'g16'
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level: 'MP2/aug-cc-pVDZ'
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keywords: 'freq=intmodes'
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keywords: 'freq'
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@@ -31,7 +31,7 @@ class Molecule:
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energy (NDArray[Any, Any]): The energy of the represented molecule
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gradient (NDArray[Any, Any]): The first derivative of the energy relative to the position
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hessian (NDArray[Any, Any]): The second derivative of the energy relative to the position
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totalMass (int): The total mass of the molecule
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total_mass (int): The total mass of the molecule
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com (NDArray[Any, Any]): The center of mass of the molecule
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"""
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@@ -50,7 +50,10 @@ class Molecule:
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self.gradient: NDArray[Any, Any]
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self.hessian: NDArray[Any, Any]
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self.totalMass: int = 0
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self.ghost_atoms: List[Atom] = []
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self.lp_atoms: List[Atom] = []
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self.total_mass: int = 0
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self.com: NDArray[Any, Any] = None
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def add_atom(self, a: Atom) -> None:
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7
diceplayer/DPpack/External/Dice.py
vendored
7
diceplayer/DPpack/External/Dice.py
vendored
@@ -27,7 +27,6 @@ class Dice:
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nprocs: int = None
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randominit = "first"
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combrule = "*"
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ncores = 1
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temp = 300.0
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press = 1.0
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@@ -35,8 +34,8 @@ class Dice:
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dens = None
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ljname = None
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outname = None
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nmol: List[int] = []
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nstep: List[int] = []
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nmol: List[int] = None
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nstep: List[int] = None
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upbuf = 360
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def __init__(self, infile: TextIO, outfile: TextIO) -> None:
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@@ -46,7 +45,7 @@ class Dice:
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@NotNull(requiredArgs=["ncores", "nmol", "dens", "nstep", "ljname", "outname"])
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def updateKeywords(self, **data):
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self.__dict__.update(data)
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self.__dict__.update(**data)
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def __new_density(self, cycle: int, proc: int) -> float:
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7
diceplayer/DPpack/External/Gaussian.py
vendored
7
diceplayer/DPpack/External/Gaussian.py
vendored
@@ -17,21 +17,18 @@ from diceplayer.DPpack.Utils.Validations import NotNull
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class Gaussian:
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qmprog = "g09"
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mem = None
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keywords = None
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chgmult = [0, 1]
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gmiddle = None # In each case, if a filename is given, its content will be
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gbottom = None # inserted in the gaussian input
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pop = "chelpg"
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level = None
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def __init__(self) -> None:
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pass
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@NotNull(requiredArgs=["level"])
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@NotNull(requiredArgs=["qmprog","level"])
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def updateKeywords(self, **data):
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self.__dict__.update(data)
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self.__dict__.update(**data)
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def run_formchk(self, cycle: int, fh: TextIO):
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@@ -21,22 +21,32 @@ env = ["OMP_STACKSIZE"]
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class Player:
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maxcyc = None
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opt = None
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nprocs = None
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qmprog = None
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lps = None
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ghosts = None
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altsteps = None
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combrule = None
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TOL_RMS_FORCE = 3e-4
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TOL_MAX_FORCE = 4.5e-4
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TOL_RMS_STEP = 1.2e-3
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TOL_MAX_SET = 1.8e-3
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TRUST_RADIUS = None
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continued: bool = False
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def __init__(self, infile: TextIO, outfile: TextIO) -> None:
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self.infile = infile
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self.outfile = outfile
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self.continued: bool = None
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self.system = System()
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self.player = self.Player()
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self.player_keywords = [
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a
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for a in dir(self.player)
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if not a.startswith("__") and not callable(getattr(self.player, a))
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]
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self.dice = Dice(infile, outfile)
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self.dice_keywords = [
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a
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@@ -51,28 +61,20 @@ class Player:
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if not a.startswith("__") and not callable(getattr(self.gaussian, a))
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]
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self.TOL_RMS_FORCE = 3e-4
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self.TOL_MAX_FORCE = 4.5e-4
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self.TOL_RMS_STEP = 1.2e-3
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self.TOL_MAX_SET = 1.8e-3
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self.TRUST_RADIUS = None
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self.combrule = None
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@NotNull(
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requiredArgs=["maxcyc", "opt", "nprocs", "qmprog", "lps", "ghosts", "altsteps"]
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)
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def updateKeywords(self, **data):
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self.__dict__.update(data)
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self.__dict__.update(**data)
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def read_keywords(self) -> None:
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with self.infile as f:
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data = yaml.load(f, Loader=yaml.SafeLoader)
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self.updateKeywords(data.get("diceplayer"))
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self.dice.updateKeywords(data.get("dice"))
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self.gaussian.updateKeywords(data.get("gaussian"))
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self.updateKeywords(**data.get("diceplayer"))
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self.dice.updateKeywords(**data.get("dice"))
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self.gaussian.updateKeywords(**data.get("gaussian"))
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def check_keywords(self) -> None:
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@@ -108,7 +110,7 @@ class Player:
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)
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# Check only if QM program is Gaussian:
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if self.player.qmprog in ("g03", "g09", "g16"):
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if self.qmprog in ("g03", "g09", "g16"):
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if self.gaussian.level == None:
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sys.exit(
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@@ -126,14 +128,14 @@ class Player:
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sys.exit("Error: file {} not found".format(self.gaussian.gbottom))
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if self.gaussian.pop != "chelpg" and (
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self.player.ghosts == "yes" or self.player.lps == "yes"
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self.ghosts == "yes" or self.lps == "yes"
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):
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sys.exit(
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"Error: ghost atoms or lone pairs only available with 'pop = chelpg')"
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)
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# Check only if QM program is Molcas:
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# if self.player.qmprog == "molcas":
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# if self.qmprog == "molcas":
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# if self.molcas.mbottom == None:
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# sys.exit("Error: 'mbottom' keyword not specified in file {}".format(self.infile))
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@@ -144,7 +146,7 @@ class Player:
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# if self.molcas.basis == None:
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# sys.exit("Error: 'basis' keyword not specified in file {}".format(self.infile))
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if self.player.altsteps != 0:
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if self.altsteps != 0:
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# Verifica se tem mais de 1 molecula QM
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# (No futuro usar o RMSD fit para poder substituir todas as moleculas QM
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@@ -155,9 +157,9 @@ class Player:
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)
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# if not zero, altsteps cannot be less than min_steps
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self.player.altsteps = max(min_steps, self.player.altsteps)
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self.altsteps = max(min_steps, self.altsteps)
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# altsteps value is always the nearest multiple of 1000
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self.player.altsteps = round(self.player.altsteps / 1000) * 1000
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self.altsteps = round(self.altsteps / 1000) * 1000
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for i in range(len(self.dice.nstep)):
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# nstep can never be less than min_steps
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@@ -198,16 +200,6 @@ class Player:
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"\n"
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)
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for key in sorted(self.player_keywords):
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if getattr(self.player, key) != None:
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if isinstance(getattr(self.player, key), list):
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string = " ".join(str(x) for x in getattr(self.player, key))
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self.outfile.write("{} = {}\n".format(key, string))
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else:
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self.outfile.write(
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"{} = {}\n".format(key, getattr(self.player, key))
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)
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self.outfile.write("\n")
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self.outfile.write(
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@@ -227,7 +219,7 @@ class Player:
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self.outfile.write("\n")
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if self.player.qmprog in ("g03", "g09", "g16"):
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if self.qmprog in ("g03", "g09", "g16"):
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self.outfile.write(
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"------------------------------------------------------------------------------------------\n"
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@@ -248,7 +240,7 @@ class Player:
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self.outfile.write("\n")
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# elif self.player.qmprog == "molcas":
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# elif self.qmprog == "molcas":
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# self.outfile.write("------------------------------------------------------------------------------------------\n"
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# " MOLCAS variables being used in this run:\n"
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@@ -492,7 +484,7 @@ class Player:
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self.outfile.write("\n")
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if self.player.ghosts == "yes" or self.player.lps == "yes":
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if self.ghosts == "yes" or self.lps == "yes":
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self.outfile.write(
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"\n"
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"------------------------------------------------------------------------------------------\n"
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@@ -585,11 +577,11 @@ class Player:
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self.dice.configure(
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StepDTO(
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self.player.initcyc,
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self.player.nprocs,
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self.player.altsteps,
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self.system.nmols,
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self.system.molecule,
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initcyc=self.initcyc,
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nprocs=self.nprocs,
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altsteps=self.altsteps,
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nmol=self.system.nmols,
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molecule=self.system.molecule,
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)
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)
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@@ -600,17 +592,17 @@ class Player:
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def gaussian_start(self, cycle: int, geomsfh: TextIO):
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self.gaussian.configure(
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self.player.initcyc,
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self.player.nprocs,
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self.initcyc,
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self.nprocs,
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self.dice.ncores,
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self.player.altsteps,
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self.player.switchcyc,
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self.player.opt,
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self.altsteps,
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self.switchcyc,
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self.opt,
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self.system.nmols,
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self.system.molecule,
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)
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position = self.gaussian.start(cycle, self.outfile, self.player.readhessian)
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position = self.gaussian.start(cycle, self.outfile, self.readhessian)
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## Update the geometry of the reference molecule
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self.system.update_molecule(position, self.outfile)
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@@ -637,7 +629,7 @@ class Player:
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else:
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nconfigs = int(self.dice.nstep[-1] / self.dice.isave)
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norm_factor = nconfigs * self.player.nprocs
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norm_factor = nconfigs * self.nprocs
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nsitesref = len(self.system.molecule[0].atom)
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# nsitesref = (
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@@ -653,7 +645,7 @@ class Player:
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thickness = []
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picked_mols = []
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for proc in range(1, self.player.nprocs + 1): # Run over folders
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for proc in range(1, self.nprocs + 1): # Run over folders
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simdir = "simfiles"
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path = (
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@@ -748,7 +740,7 @@ class Player:
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asec_charges[-1]["rz"] = atom.rz
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asec_charges[-1]["chg"] = atom.chg / norm_factor
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# if self.player.vdwforces == "yes":
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# if self.vdwforces == "yes":
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# vdw_meanfield[-1]["rx"] = atom["rx"]
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# vdw_meanfield[-1]["ry"] = atom["ry"]
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# vdw_meanfield[-1]["rz"] = atom["rz"]
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@@ -810,22 +802,3 @@ class Player:
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otherfh.close()
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return asec_charges
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class Player:
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def __init__(self) -> None:
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self.maxcyc = None
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self.nprocs = 1
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self.switchcyc = 3
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self.altsteps = 20000
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self.maxstep = 0.3
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self.opt = "yes"
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self.freq = "no"
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self.readhessian = "no"
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self.lps = "no"
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self.ghosts = "no"
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self.vdwforces = "no"
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self.tol_factor = 1.2
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self.qmprog = "g16"
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self.initcyc = 1
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@@ -7,11 +7,12 @@ from diceplayer.DPpack.Environment.Molecule import Molecule
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@dataclass
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class StepDTO:
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initcyc: int
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nprocs: int
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ncores: int
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altsteps: int
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switchcyc: int
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opt: str
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nmol: List[int]
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molecule: List[Molecule]
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cycle: int = None
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initcyc: int = None
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nprocs: int = None
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ncores: int = None
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altsteps: int = None
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switchcyc: int = None
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opt: str = None
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nmol: List[int] = None
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molecule: List[Molecule] = None
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@@ -4,21 +4,15 @@ import argparse
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import os
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import pickle
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import shutil
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import signal
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import sys
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import time
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from multiprocessing import Process, connection
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import numpy as np
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import setproctitle
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from diceplayer.DPpack.Environment.Atom import Atom
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from diceplayer.DPpack.Environment.Molecule import Molecule
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from diceplayer.DPpack.Player import Player
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from diceplayer.DPpack.Utils.Misc import *
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__version = "dev"
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setproctitle.setproctitle("diceplayer-{}".format(__version))
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__VERSION = "dev"
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setproctitle.setproctitle("diceplayer-{}".format(__VERSION))
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if __name__ == "__main__":
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#### Read and store the arguments passed to the program ####
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@@ -29,12 +23,12 @@ if __name__ == "__main__":
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"--continue", dest="opt_continue", default=False, action="store_true"
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)
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parser.add_argument(
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"--version", action="version", version="diceplayer-" + __version
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"--version", action="version", version="diceplayer-" + __VERSION
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)
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parser.add_argument(
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"-i",
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dest="infile",
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default="control.in",
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default="control.yml",
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metavar="INFILE",
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help="input file of diceplayer [default = control.in]",
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)
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@@ -90,9 +84,10 @@ if __name__ == "__main__":
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player.print_keywords()
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if args.opt_continue:
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player.player.initcyc = save[0] + 1
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player.initcyc = save[0] + 1
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player.system = save[1]
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else:
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player.initcyc = 1
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player.read_potential()
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#### Check whether the executables are in the path
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@@ -126,13 +121,13 @@ if __name__ == "__main__":
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make_simulation_dir()
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else:
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simdir = "simfiles"
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stepdir = "step{:02d}".format(player.player.initcyc)
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stepdir = "step{:02d}".format(player.initcyc)
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if os.path.exists(simdir + os.sep + stepdir):
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shutil.rmtree(simdir + os.sep + stepdir)
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#### Open the geoms.xyz file and prints the initial geometry if starting from zero
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if player.player.initcyc == 1:
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if player.initcyc == 1:
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try:
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path = "geoms.xyz"
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geomsfh = open(path, "w", 1)
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@@ -153,8 +148,8 @@ if __name__ == "__main__":
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position = player.system.molecule[0].read_position()
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## If restarting, read the last gradient and hessian
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# if player.player.initcyc > 1:
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# if player.player.qmprog in ("g03", "g09", "g16"):
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# if player.initcyc > 1:
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# if player.qmprog in ("g03", "g09", "g16"):
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# Gaussian.read_forces("grad_hessian.dat")
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# Gaussian.read_hessian_fchk("grad_hessian.dat")
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@@ -168,9 +163,7 @@ if __name__ == "__main__":
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||||
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player.outfile.write("\n" + 90 * "-" + "\n")
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||||
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for cycle in range(
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player.player.initcyc, player.player.initcyc + player.player.maxcyc
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):
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for cycle in range(player.initcyc, player.initcyc + player.maxcyc):
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||||
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||||
player.outfile.write("{} Step # {}\n".format(40 * " ", cycle))
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||||
player.outfile.write(90 * "-" + "\n\n")
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||||
@@ -192,7 +185,7 @@ if __name__ == "__main__":
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||||
asec_charges = player.populate_asec_vdw(cycle)
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||||
|
||||
## After ASEC is built, compress files bigger than 1MB
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||||
for proc in range(1, player.player.nprocs + 1):
|
||||
for proc in range(1, player.nprocs + 1):
|
||||
path = "step{:02d}".format(cycle) + os.sep + "p{:02d}".format(proc)
|
||||
compress_files_1mb(path)
|
||||
|
||||
|
||||
15
geoms.xyz
15
geoms.xyz
@@ -1,15 +0,0 @@
|
||||
Cycle # 0
|
||||
Number of site: 12
|
||||
C 1.400000 0.000000 0.000000
|
||||
C 0.700000 1.212436 0.000000
|
||||
C -0.700000 1.212436 0.000000
|
||||
C -1.400000 0.000000 0.000000
|
||||
C -0.700000 -1.212436 0.000000
|
||||
C 0.700000 -1.212436 0.000000
|
||||
H 2.488100 0.000000 0.000000
|
||||
H 1.244000 2.154671 0.000000
|
||||
H -1.244000 2.154671 0.000000
|
||||
H -2.488100 0.000000 0.000000
|
||||
H -1.244000 -2.154671 0.000000
|
||||
H 1.244000 -2.154671 0.000000
|
||||
----------------------------------------
|
||||
@@ -1,18 +1,18 @@
|
||||
*
|
||||
2
|
||||
12 BENZENO
|
||||
1 6 0.000000 1.400000 0.000000 0.00000000 0.1100 3.7500
|
||||
1 6 1.212436 0.700000 0.000000 0.00000000 0.1100 3.7500
|
||||
1 6 1.212436 -0.700000 0.000000 0.00000000 0.1100 3.7500
|
||||
1 6 0.000000 -1.400000 0.000000 0.00000000 0.1100 3.7500
|
||||
1 6 -1.212436 -0.700000 0.000000 0.00000000 0.1100 3.7500
|
||||
1 6 -1.212436 0.700000 0.000000 0.00000000 0.1100 3.7500
|
||||
2 1 0.000000 2.488100 0.000000 0.00000000 0.0000 0.0000
|
||||
2 1 2.154671 1.244000 0.000000 0.00000000 0.0000 0.0000
|
||||
2 1 2.154671 -1.244000 0.000000 0.00000000 0.0000 0.0000
|
||||
2 1 0.000000 -2.488100 0.000000 0.00000000 0.0000 0.0000
|
||||
2 1 -2.154671 -1.244000 0.000000 0.00000000 0.0000 0.0000
|
||||
2 1 -2.154671 1.244000 0.000000 0.00000000 0.0000 0.0000
|
||||
1 6 1.407784 0.000000 0.000000 0.00000000 0.1100 3.7500
|
||||
1 6 0.796966 1.274231 -0.338230 0.00000000 0.1100 3.7500
|
||||
1 6 -0.703892 1.219173 -0.000000 0.00000000 0.1100 3.7500
|
||||
1 6 -1.389932 -0.018988 0.227698 0.00000000 0.1100 3.7500
|
||||
1 6 -0.703892 -1.219173 0.000000 0.00000000 0.1100 3.7500
|
||||
1 6 0.703892 -1.219173 0.000000 0.00000000 0.1100 3.7500
|
||||
2 1 2.501890 -0.000000 0.000000 0.00000000 0.0000 0.0000
|
||||
2 1 1.415017 2.294961 -0.608843 0.00000000 0.0000 0.0000
|
||||
2 1 -1.250943 2.166698 -0.000000 0.00000000 0.0000 0.0000
|
||||
2 1 -2.501890 0.000000 0.000000 0.00000000 0.0000 0.0000
|
||||
2 1 -0.519043 -2.235211 0.017991 0.00000000 0.0000 0.0000
|
||||
2 1 1.250943 -2.166698 -0.000000 0.00000000 0.0000 0.0000
|
||||
16 PLACEHOLDER
|
||||
1 6 0.672026 -2.823446 0.002631 -0.11500000 0.0700 3.5500
|
||||
1 6 2.072026 -2.823446 0.002631 -0.11500000 0.0700 3.5500
|
||||
Reference in New Issue
Block a user