pysep.io.nml.physics package¶

Subpackages¶

pysep.io.nml.physics.defaults package
- Module contents
  - Avalible Control Namelist Files

Submodules¶

pysep.io.nml.physics.paramConstruct module¶

Author: Thomas M. Boudreaux

Created: June 2022

Last Modified: June 2022

Dataclasses for physics namelist files. I have transcibed all the default values laied out in the data statements from Parmin.f into dataclasses.

Parameters that are scalers are represented as fields, parameters which are lists/vectors are represented by their own dataclasses. This is primarly to allow for more easily changing / setting values in these lists without having to write out the entire list

Examples

Here we have an example where we want to update just the max fractional timestep, as defined in ATIME. We can load the ATIMEd dataclass with all default parameters except the maxFractionalTimestepChange

>>> from pysep.io.nml.physics import ATIMEd
>>> from pysep.io.nml.physics.defaults import phys1
>>> phys1['atime'] = ATIMEd(maxFractionalTimestepChange=1.04).as_list()
>>> phys1.save("ExampleUpdatedPhysics.nml")

We also know that the DSEP doc defines these in terms of index not names, so if we want to modify the parameters of ATIMEd based on index we can also do that

>>> from pysep.io.nml.physics import ATIMEd
>>> from pysep.io.nml.physics.defaults import phys1
>>> ATIME = ATIMEd()
>>> ATIME[13] = 1.04
>>> phys1['atime'] = ATIME.as_list()
>>> phys1.save("ExampleUpdatedPhysics.nml")

class pysep.io.nml.physics.paramConstruct.ANEWCPd(rs1: str = ' ', rs2: str = ' ', rs3: str = ' ', rs4: str = ' ', rs5: str = ' ', rs6: str = ' ', rs7: str = ' ', rs8: str = ' ', rs9: str = ' ', rs10: str = ' ', rs11: str = ' ', rs12: str = ' ')¶

Bases: object

as_list() → list¶

Return a list representation of ANEWCP

Returns: outList – list in the correct order for DSEP to interpet
Return type: list[str]

rs1: str = ' '¶

rs10: str = ' '¶

rs11: str = ' '¶

rs12: str = ' '¶

rs2: str = ' '¶

rs3: str = ' '¶

rs4: str = ' '¶

rs5: str = ' '¶

rs6: str = ' '¶

rs7: str = ' '¶

rs8: str = ' '¶

rs9: str = ' '¶

class pysep.io.nml.physics.paramConstruct.ATIMEd(minCentralXBeforeHBurning: float = 0.001, maxChangeXforCoreHBurning: float = 0.02, maxFractionalChangeCentral: float = 0.5, maxChangeYCentral: float = 0.02, maxFractionalChangeYCentral: float = 0.03, maxMassAllowedToBurnInShell: float = 0.0015, maxDepletionInXAtMidpointOfHShell: float = 0.1, maxChangeP: float = 0.005, maxChangeT: float = 0.01, maxChangeR: float = 0.005, maxChangeL: float = 0.005, maxPercentageTimestepChange: float = 0.25, maxFractionalTimestepChange: float = 1.01, maxAbsoluteTimestepChange: float = - 10000000.0)¶

Bases: object

as_list() → list¶

Return a list representation of ATIME

Returns: outList – list in the correct order for DSEP to interpet
Return type: list[float]

from_list(l: list)¶

maxAbsoluteTimestepChange: float = -10000000.0¶

maxChangeL: float = 0.005¶

maxChangeP: float = 0.005¶

maxChangeR: float = 0.005¶

maxChangeT: float = 0.01¶

maxChangeXforCoreHBurning: float = 0.02¶

maxChangeYCentral: float = 0.02¶

maxDepletionInXAtMidpointOfHShell: float = 0.1¶

maxFractionalChangeCentral: float = 0.5¶

maxFractionalChangeYCentral: float = 0.03¶

maxFractionalTimestepChange: float = 1.01¶

maxMassAllowedToBurnInShell: float = 0.0015¶

maxPercentageTimestepChange: float = 0.25¶

minCentralXBeforeHBurning: float = 0.001¶

class pysep.io.nml.physics.paramConstruct.HTOLERd(convCritDeltaLogP: float = 6e-05, convCritDeltaLogT: float = 4.5e-05, convCritDeltaLLsun: float = 0.003, convCritHeBurning: float = 9e-05, convTolerLogPLogR: float = 3e-05, maxCorrectionDeltaLogP: float = 0.9, maxCorrectionDeltaLogT: float = 0.5, maxCorrectionDeltaLLsun: float = 0.5, maxCorrectionDeltaR: float = 2.0, convTolerRHSofTL: float = 2.5e-06)¶

Bases: object

as_list() → list¶

Return a list representation of HTOLER

Returns: outList – list in the correct order for DSEP to interpet
Return type: list[list[float]]

convCritDeltaLLsun: float = 0.003¶

convCritDeltaLogP: float = 6e-05¶

convCritDeltaLogT: float = 4.5e-05¶

convCritHeBurning: float = 9e-05¶

convTolerLogPLogR: float = 3e-05¶

convTolerRHSofTL: float = 2.5e-06¶

maxCorrectionDeltaLLsun: float = 0.5¶

maxCorrectionDeltaLogP: float = 0.9¶

maxCorrectionDeltaLogT: float = 0.5¶

maxCorrectionDeltaR: float = 2.0¶

class pysep.io.nml.physics.paramConstruct.IEOSd(if1: int = 1, if2: int = 101, if3: int = 0)¶

Bases: object

as_list() → list¶

Return a list representation of IEOS

Returns: outList – list in the correct order for DSEP to interpet
Return type: list[int]

if1: int = 1¶

if2: int = 101¶

if3: int = 0¶

set_eos(eos: str)¶

Sets the equation of states control flags to the 5 defined equations of state from Irwin

Parameters: eos (str) – equation of state name (from Irwin / free_eos.f). This can be either EOS1, EOS1A, EOS2, EOS3, or EOS4. Case insensitive.
Raises: KeyError – if eos is not one of the defined equaitons of state

class pysep.io.nml.physics.paramConstruct.SHELLTOLd(minChangeLogM: float = 1e-08, maxChangeLogM: float = 0.08, DeltaXReqToFlag: float = 0.05, DeltaYReqToFlag: float = 1.0, maxDisconX: float = 1.0, maxDisconZ: float = 1.0, dLogPEtxtenBelowOvershootAboveBaseSufraceCZ: float = 0.0, maxdLogPSurfCZAboveFineMeshZone: float = 0.05, maxChangeLLsun: float = 0.02, maxdLogPInFineMeshZone: float = 0.05, maxdLogPBelowSurfCZBelowFineMeshZone: float = 0.05, maxdLogOmega: float = 0.1)¶

Bases: object

DeltaXReqToFlag: float = 0.05¶

DeltaYReqToFlag: float = 1.0¶

as_list() → list¶

Return a list representation of SHELLTOL

Returns: outList – list in the correct order for DSEP to interpet
Return type: list[float]

dLogPEtxtenBelowOvershootAboveBaseSufraceCZ: float = 0.0¶

maxChangeLLsun: float = 0.02¶

maxChangeLogM: float = 0.08¶

maxDisconX: float = 1.0¶

maxDisconZ: float = 1.0¶

maxdLogOmega: float = 0.1¶

maxdLogPBelowSurfCZBelowFineMeshZone: float = 0.05¶

maxdLogPInFineMeshZone: float = 0.05¶

maxdLogPSurfCZAboveFineMeshZone: float = 0.05¶

minChangeLogM: float = 1e-08¶

class pysep.io.nml.physics.paramConstruct.SSTANSARDd(SS1: float = 0.9828, SS2: float = 1.0485, SS3: float = 0.9815, SS4: float = 0.9241, SS5: float = 1.3818, SS6: float = 1.0542, SS7: float = 1.0, SS8: float = 1.0, SS9: float = 1.0, SS10: float = 1.0, SS11: float = 1.0, SS12: float = 1.0, SS13: float = 1.0, SS14: float = 1.0, SS15: float = 1.0108, SS16: float = 0.7819, SS17: float = 0.2875, SS18: float = 1.0, SS19: float = 1.0)¶

Bases: object

SS1: float = 0.9828¶

SS10: float = 1.0¶

SS11: float = 1.0¶

SS12: float = 1.0¶

SS13: float = 1.0¶

SS14: float = 1.0¶

SS15: float = 1.0108¶

SS16: float = 0.7819¶

SS17: float = 0.2875¶

SS18: float = 1.0¶

SS19: float = 1.0¶

SS2: float = 1.0485¶

SS3: float = 0.9815¶

SS4: float = 0.9241¶

SS5: float = 1.3818¶

SS6: float = 1.0542¶

SS7: float = 1.0¶

SS8: float = 1.0¶

SS9: float = 1.0¶

as_list() → list¶

Return a list representation of SSTANSARD

Returns: outList – list in the correct order for DSEP to interpet
Return type: list[float]

class pysep.io.nml.physics.paramConstruct.TCUTd(lowTempCuttoffAll: float = 6.5, lowTempCuttoffPP: float = 6.5, lowTempCuttoffCNO: float = 6.82, lowTempCuttoffHe: float = 7.73, lowTempCuttoffNuEmission: float = 7.5)¶

Bases: object

as_list() → list¶

Return a list representation of TCUT

Returns: outList – list in the correct order for DSEP to interpet
Return type: list[float]

lowTempCuttoffAll: float = 6.5¶

lowTempCuttoffCNO: float = 6.82¶

lowTempCuttoffHe: float = 7.73¶

lowTempCuttoffNuEmission: float = 7.5¶

lowTempCuttoffPP: float = 6.5¶

class pysep.io.nml.physics.paramConstruct.base(ATMMIN: float = 0.1, ATMBEG: float = 0.1, ATMERR: float = 0.0003, ATMMAX: float = 0.5, ATMD0: float = 1e-10, ANEWCP: pysep.io.nml.physics.paramConstruct.ANEWCPd = ANEWCPd(rs1=' ', rs2=' ', rs3=' ', rs4=' ', rs5=' ', rs6=' ', rs7=' ', rs8=' ', rs9=' ', rs10=' ', rs11=' ', rs12=' '), ATMP: str = 'REL', ACFPFT: float = 1e-36, ATIME: pysep.io.nml.physics.paramConstruct.ATIMEd = ATIMEd(minCentralXBeforeHBurning=0.001, maxChangeXforCoreHBurning=0.02, maxFractionalChangeCentral=0.5, maxChangeYCentral=0.02, maxFractionalChangeYCentral=0.03, maxMassAllowedToBurnInShell=0.0015, maxDepletionInXAtMidpointOfHShell=0.1, maxChangeP=0.005, maxChangeT=0.01, maxChangeR=0.005, maxChangeL=0.005, maxPercentageTimestepChange=0.25, maxFractionalTimestepChange=1.01, maxAbsoluteTimestepChange=- 10000000.0), ALPHAC: float = 0.0, ALPHAE: float = 0.0, ALFA: float = 1.5, ALPHAM: float = 0.0, ATMSTP: float = 0.5, ABSTOL: float = 1e-05, CMIN: float = 1e-20, CLSUN: float = 3.828e+33, CRSUN: float = 69570000000.0, DPENV: float = 1.0, DTDIF: float = 0.01, DTWIND: float = 10.0, DJOK: float = 0.0001, DT_GS: float = 0.1, ENVERR: float = 0.0003, ENVMAX: float = 0.5, ENVMIN: float = 0.1, ENVBEG: float = 0.1, ENVSTP: float = 0.5, ETADH0: float = - 1.0, ETADH1: float = 1.0, FCORR0: float = 0.8, FCORRI: float = 0.1, FK: float = 1.0, FW: float = 1.0, FC: float = 1.0, FO: float = 1.0, FMU: float = 1.0, FES: float = 1.0, FCORE: float = 1.0, FGSF: float = 1.0, FSS: float = 1.0, FESC: float = 1.0, FSSC: float = 1.0, FGSFC: float = 1.0, FGRY: float = 1.0, FGRZ: float = 1.0, GRTOL: float = 1e-08, HTOLER: pysep.io.nml.physics.paramConstruct.HTOLERd = HTOLERd(convCritDeltaLogP=6e-05, convCritDeltaLogT=4.5e-05, convCritDeltaLLsun=0.003, convCritHeBurning=9e-05, convTolerLogPLogR=3e-05, maxCorrectionDeltaLogP=0.9, maxCorrectionDeltaLogT=0.5, maxCorrectionDeltaLLsun=0.5, maxCorrectionDeltaR=2.0, convTolerRHSofTL=2.5e-06), ITFP1: int = 5, ITFP2: int = 20, IMAX: int = 11, ITDIF1: int = 1, ITDIF2: int = 1, IES: int = 1, IGSF: int = 1, IMU: int = 1, ILAMBDA: int = 1, IEOS: pysep.io.nml.physics.paramConstruct.IEOSd = IEOSd(if1=1, if2=101, if3=0), KTTAU: int = 0, KEMMAX: int = 50, LCOREL: bool = False, LVFC: bool = False, LDIFZ: bool = False, LNEWCP: bool = False, LKUTHE: bool = False, LOVSTC: bool = False, LOVSTE: bool = False, LOVSTM: bool = False, LROT: bool = False, LNEW0: bool = False, LINSTB: bool = False, LWNEW: bool = False, LJDOT0: bool = False, LENVG: bool = False, LNULOS1: bool = False, LTHOUL: bool = False, LCORE: bool = False, LNEWS: bool = False, LISUN: float = 1.45e-11, LSOLID: bool = False, MCORE: int = 0, NITER1: int = 2, NITER2: int = 20, NITER3: int = 2, NITER4: int = 0, NUSE: int = 7, NITER_GS: int = 10, OPTOL: float = 1e-08, OMEGASUN: float = 2.865e-06, RCRIT: float = 1000.0, RELTOL: float = 0.0001, STOLR0: float = 0.001, SHELLTOL: pysep.io.nml.physics.paramConstruct.SHELLTOLd = SHELLTOLd(minChangeLogM=1e-08, maxChangeLogM=0.08, DeltaXReqToFlag=0.05, DeltaYReqToFlag=1.0, maxDisconX=1.0, maxDisconZ=1.0, dLogPEtxtenBelowOvershootAboveBaseSufraceCZ=0.0, maxdLogPSurfCZAboveFineMeshZone=0.05, maxChangeLLsun=0.02, maxdLogPInFineMeshZone=0.05, maxdLogPBelowSurfCZBelowFineMeshZone=0.05, maxdLogOmega=0.1), TCUT: pysep.io.nml.physics.paramConstruct.TCUTd = TCUTd(lowTempCuttoffAll=6.5, lowTempCuttoffPP=6.5, lowTempCuttoffCNO=6.82, lowTempCuttoffHe=7.73, lowTempCuttoffNuEmission=7.5), TSCUT: float = 6.0, TENV0: float = 3.0, TENV1: float = 9.0, TGCUT: float = 6.9, TRIDT: float = 0.01, TRIDL: float = 0.08, TOLLFK: float = 0.0001, TOLLFC: float = 0.0001, WALPCZ: float = 0.0, WNEW: float = 0.0, XMIN: float = 0.001, YMIN: float = 0.001, SSTANSARD: pysep.io.nml.physics.paramConstruct.SSTANSARDd = SSTANSARDd(SS1=0.9828, SS2=1.0485, SS3=0.9815, SS4=0.9241, SS5=1.3818, SS6=1.0542, SS7=1.0, SS8=1.0, SS9=1.0, SS10=1.0, SS11=1.0, SS12=1.0, SS13=1.0, SS14=1.0, SS15=1.0108, SS16=0.7819, SS17=0.2875, SS18=1.0, SS19=1.0), WEAKSCREENING: float = 0.03, LDIFAD: int = False, LNOJ: int = False, SENV0A: int = False, ZENV0: float = 0.02, LSTORE: int = False, NPENV: int = 20, NPRTPT: int = 1, NMODLS: int = 1, NBN: float = 1.0, RSCLCM: float = 1.0, ZSI: float = 0.0, HPTTOL: int = 1, XNEWCP: int = False, LPTIME: int = True, CMIXL: float = 1.72, BETAC: float = 0.0, LADOV: int = False, LEXCOM: int = False, LPULSE: int = False, IPVER: int = 2, LDIFY: int = False, LSNU: int = False, LTHOULFIT: int = False, LDH: int = False, LSEMIC: int = False, LISO: int = False, LNULOS2: int = False, LOPALE: int = False, IAFE: int = 0, LSCV: int = False, LZAMFIT: int = True, LHAFT: int = False, LOPCOEF: int = False, FO95COBIN: str = '/Users/aaron/dsep/run/OPAL_GS98.bin', LHB: int = False, LFREE_EOS: int = False, LUSENEWPHX: int = False)¶

Bases: object

ABSTOL: float = 1e-05¶

ACFPFT: float = 1e-36¶

ALFA: float = 1.5¶

ALPHAC: float = 0.0¶

ALPHAE: float = 0.0¶

ALPHAM: float = 0.0¶

ANEWCP: pysep.io.nml.physics.paramConstruct.ANEWCPd = ANEWCPd(rs1=' ', rs2=' ', rs3=' ', rs4=' ', rs5=' ', rs6=' ', rs7=' ', rs8=' ', rs9=' ', rs10=' ', rs11=' ', rs12=' ')¶

ATIME: pysep.io.nml.physics.paramConstruct.ATIMEd = ATIMEd(minCentralXBeforeHBurning=0.001, maxChangeXforCoreHBurning=0.02, maxFractionalChangeCentral=0.5, maxChangeYCentral=0.02, maxFractionalChangeYCentral=0.03, maxMassAllowedToBurnInShell=0.0015, maxDepletionInXAtMidpointOfHShell=0.1, maxChangeP=0.005, maxChangeT=0.01, maxChangeR=0.005, maxChangeL=0.005, maxPercentageTimestepChange=0.25, maxFractionalTimestepChange=1.01, maxAbsoluteTimestepChange=-10000000.0)¶

ATMBEG: float = 0.1¶

ATMD0: float = 1e-10¶

ATMERR: float = 0.0003¶

ATMMAX: float = 0.5¶

ATMMIN: float = 0.1¶

ATMP: str = 'REL'¶

ATMSTP: float = 0.5¶

BETAC: float = 0.0¶

CLSUN: float = 3.828e+33¶

CMIN: float = 1e-20¶

CMIXL: float = 1.72¶

CRSUN: float = 69570000000.0¶

DJOK: float = 0.0001¶

DPENV: float = 1.0¶

DTDIF: float = 0.01¶

DTWIND: float = 10.0¶

DT_GS: float = 0.1¶

ENVBEG: float = 0.1¶

ENVERR: float = 0.0003¶

ENVMAX: float = 0.5¶

ENVMIN: float = 0.1¶

ENVSTP: float = 0.5¶

ETADH0: float = -1.0¶

ETADH1: float = 1.0¶

FC: float = 1.0¶

FCORE: float = 1.0¶

FCORR0: float = 0.8¶

FCORRI: float = 0.1¶

FES: float = 1.0¶

FESC: float = 1.0¶

FGRY: float = 1.0¶

FGRZ: float = 1.0¶

FGSF: float = 1.0¶

FGSFC: float = 1.0¶

FK: float = 1.0¶

FMU: float = 1.0¶

FO: float = 1.0¶

FO95COBIN: str = '/Users/aaron/dsep/run/OPAL_GS98.bin'¶

FSS: float = 1.0¶

FSSC: float = 1.0¶

FW: float = 1.0¶

GRTOL: float = 1e-08¶

HPTTOL: int = 1¶

HTOLER: pysep.io.nml.physics.paramConstruct.HTOLERd = HTOLERd(convCritDeltaLogP=6e-05, convCritDeltaLogT=4.5e-05, convCritDeltaLLsun=0.003, convCritHeBurning=9e-05, convTolerLogPLogR=3e-05, maxCorrectionDeltaLogP=0.9, maxCorrectionDeltaLogT=0.5, maxCorrectionDeltaLLsun=0.5, maxCorrectionDeltaR=2.0, convTolerRHSofTL=2.5e-06)¶

IAFE: int = 0¶

IEOS: pysep.io.nml.physics.paramConstruct.IEOSd = IEOSd(if1=1, if2=101, if3=0)¶

IES: int = 1¶

IGSF: int = 1¶

ILAMBDA: int = 1¶

IMAX: int = 11¶

IMU: int = 1¶

IPVER: int = 2¶

ITDIF1: int = 1¶

ITDIF2: int = 1¶

ITFP1: int = 5¶

ITFP2: int = 20¶

KEMMAX: int = 50¶

KTTAU: int = 0¶

LADOV: int = False¶

LCORE: bool = False¶

LCOREL: bool = False¶

LDH: int = False¶

LDIFAD: int = False¶

LDIFY: int = False¶

LDIFZ: bool = False¶

LENVG: bool = False¶

LEXCOM: int = False¶

LFREE_EOS: int = False¶

LHAFT: int = False¶

LHB: int = False¶

LINSTB: bool = False¶

LISO: int = False¶

LISUN: float = 1.45e-11¶

LJDOT0: bool = False¶

LKUTHE: bool = False¶

LNEW0: bool = False¶

LNEWCP: bool = False¶

LNEWS: bool = False¶

LNOJ: int = False¶

LNULOS1: bool = False¶

LNULOS2: int = False¶

LOPALE: int = False¶

LOPCOEF: int = False¶

LOVSTC: bool = False¶

LOVSTE: bool = False¶

LOVSTM: bool = False¶

LPTIME: int = True¶

LPULSE: int = False¶

LROT: bool = False¶

LSCV: int = False¶

LSEMIC: int = False¶

LSNU: int = False¶

LSOLID: bool = False¶

LSTORE: int = False¶

LTHOUL: bool = False¶

LTHOULFIT: int = False¶

LUSENEWPHX: int = False¶

LVFC: bool = False¶

LWNEW: bool = False¶

LZAMFIT: int = True¶

MCORE: int = 0¶

NBN: float = 1.0¶

NITER1: int = 2¶

NITER2: int = 20¶

NITER3: int = 2¶

NITER4: int = 0¶

NITER_GS: int = 10¶

NMODLS: int = 1¶

NPENV: int = 20¶

NPRTPT: int = 1¶

NUSE: int = 7¶

OMEGASUN: float = 2.865e-06¶

OPTOL: float = 1e-08¶

RCRIT: float = 1000.0¶

RELTOL: float = 0.0001¶

RSCLCM: float = 1.0¶

SENV0A: int = False¶

SHELLTOL: pysep.io.nml.physics.paramConstruct.SHELLTOLd = SHELLTOLd(minChangeLogM=1e-08, maxChangeLogM=0.08, DeltaXReqToFlag=0.05, DeltaYReqToFlag=1.0, maxDisconX=1.0, maxDisconZ=1.0, dLogPEtxtenBelowOvershootAboveBaseSufraceCZ=0.0, maxdLogPSurfCZAboveFineMeshZone=0.05, maxChangeLLsun=0.02, maxdLogPInFineMeshZone=0.05, maxdLogPBelowSurfCZBelowFineMeshZone=0.05, maxdLogOmega=0.1)¶

SSTANSARD: pysep.io.nml.physics.paramConstruct.SSTANSARDd = SSTANSARDd(SS1=0.9828, SS2=1.0485, SS3=0.9815, SS4=0.9241, SS5=1.3818, SS6=1.0542, SS7=1.0, SS8=1.0, SS9=1.0, SS10=1.0, SS11=1.0, SS12=1.0, SS13=1.0, SS14=1.0, SS15=1.0108, SS16=0.7819, SS17=0.2875, SS18=1.0, SS19=1.0)¶

STOLR0: float = 0.001¶

TCUT: pysep.io.nml.physics.paramConstruct.TCUTd = TCUTd(lowTempCuttoffAll=6.5, lowTempCuttoffPP=6.5, lowTempCuttoffCNO=6.82, lowTempCuttoffHe=7.73, lowTempCuttoffNuEmission=7.5)¶

TENV0: float = 3.0¶

TENV1: float = 9.0¶

TGCUT: float = 6.9¶

TOLLFC: float = 0.0001¶

TOLLFK: float = 0.0001¶

TRIDL: float = 0.08¶

TRIDT: float = 0.01¶

TSCUT: float = 6.0¶

WALPCZ: float = 0.0¶

WEAKSCREENING: float = 0.03¶

WNEW: float = 0.0¶

XMIN: float = 0.001¶

XNEWCP: int = False¶

YMIN: float = 0.001¶

ZENV0: float = 0.02¶

ZSI: float = 0.0¶

as_dict() → dict¶

class pysep.io.nml.physics.paramConstruct.lowmass(ATMMIN: float = 0.015, ATMBEG: float = 0.015, ATMERR: float = 1e-05, ATMMAX: float = 0.05, ATMD0: float = 1e-10, ANEWCP: str = ' ', ATMP: str = 'REL', ACFPFT: float = 1e-36, ATIME: pysep.io.nml.physics.paramConstruct.ATIMEd = ATIMEd(minCentralXBeforeHBurning=0.0001, maxChangeXforCoreHBurning=0.02, maxFractionalChangeCentral=0.2, maxChangeYCentral=0.02, maxFractionalChangeYCentral=0.03, maxMassAllowedToBurnInShell=0.0015, maxDepletionInXAtMidpointOfHShell=0.1, maxChangeP=0.02, maxChangeT=0.4, maxChangeR=0.02, maxChangeL=0.02, maxPercentageTimestepChange=0.25, maxFractionalTimestepChange=1.01, maxAbsoluteTimestepChange=- 10000000.0), ALPHAC: float = 0.0, ALPHAE: float = 0.0, ALFA: float = 1.5, ALPHAM: float = 0.0, ATMSTP: float = 0.01, ABSTOL: float = 1e-06, CMIN: float = 1e-20, CLSUN: float = 3.8418e+33, CRSUN: float = 69598000000.0, DPENV: float = 1.0, DTDIF: float = 0.01, DTWIND: float = 10.0, DJOK: float = 0.0001, DT_GS: float = 0.1, ENVERR: float = 1e-05, ENVMAX: float = 0.05, ENVMIN: float = 0.015, ENVBEG: float = 0.015, ENVSTP: float = 0.01, ETADH0: float = - 1.0, ETADH1: float = 1.0, FCORR0: float = 0.8, FCORRI: float = 0.1, FK: float = 1.0, FW: float = 1.0, FC: float = 1.0, FO: float = 1.0, FMU: float = 1.0, FES: float = 1.0, FCORE: float = 1.0, FGSF: float = 1.0, FSS: float = 1.0, FESC: float = 1.0, FSSC: float = 1.0, FGSFC: float = 1.0, FGRY: float = 1.0, FGRZ: float = 1.0, GRTOL: float = 2e-07, HTOLER: pysep.io.nml.physics.paramConstruct.HTOLERd = HTOLERd(convCritDeltaLogP=6e-05, convCritDeltaLogT=4.5e-05, convCritDeltaLLsun=0.003, convCritHeBurning=9e-05, convTolerLogPLogR=3e-05, maxCorrectionDeltaLogP=90000.0, maxCorrectionDeltaLogT=50000.0, maxCorrectionDeltaLLsun=50000.0, maxCorrectionDeltaR=50000000000.0, convTolerRHSofTL=2.5e-06), ITFP1: int = 5, ITFP2: int = 20, IMAX: int = 11, ITDIF1: int = 1, ITDIF2: int = 1, IES: int = 1, IGSF: int = 1, IMU: int = 1, ILAMBDA: int = 4, IEOS: pysep.io.nml.physics.paramConstruct.IEOSd = IEOSd(if1=1, if2=101, if3=0), KTTAU: int = 0, KEMMAX: int = 50, LCOREL: bool = True, LVFC: bool = False, LDIFZ: bool = False, LNEWCP: bool = False, LKUTHE: bool = False, LOVSTC: bool = False, LOVSTE: bool = True, LOVSTM: bool = False, LROT: bool = False, LNEW0: bool = True, LINSTB: bool = False, LWNEW: bool = False, LJDOT0: bool = False, LENVG: bool = False, LNULOS1: bool = True, LTHOUL: bool = False, LCORE: bool = False, LNEWS: bool = True, LISUN: float = 1.45e-11, LSOLID: bool = False, MCORE: int = 1, NITER1: int = 2, NITER2: int = 40, NITER3: int = 0, NITER4: int = 0, NUSE: int = 7, NITER_GS: int = 10, OPTOL: float = 1e-08, OMEGASUN: float = 2.865e-06, RCRIT: float = 1000.0, RELTOL: float = 1e-05, STOLR0: float = 1e-07, SHELLTOL: pysep.io.nml.physics.paramConstruct.SHELLTOLd = SHELLTOLd(minChangeLogM=1e-10, maxChangeLogM=0.05, DeltaXReqToFlag=0.02, DeltaYReqToFlag=1.0, maxDisconX=1.0, maxDisconZ=1.0, dLogPEtxtenBelowOvershootAboveBaseSufraceCZ=0.0, maxdLogPSurfCZAboveFineMeshZone=0.01, maxChangeLLsun=0.01, maxdLogPInFineMeshZone=0.02, maxdLogPBelowSurfCZBelowFineMeshZone=0.02, maxdLogOmega=0.1), TCUT: pysep.io.nml.physics.paramConstruct.TCUTd = TCUTd(lowTempCuttoffAll=6.5, lowTempCuttoffPP=6.5, lowTempCuttoffCNO=6.82, lowTempCuttoffHe=7.73, lowTempCuttoffNuEmission=7.5), TSCUT: float = 6.0, TENV0: float = 3.0, TENV1: float = 9.0, TGCUT: float = 6.9, TRIDT: float = 0.001, TRIDL: float = 8000.0, TOLLFK: float = 0.0001, TOLLFC: float = 0.0001, WALPCZ: float = 0.0, WNEW: float = 0.0, XMIN: float = 0.001, YMIN: float = 0.001, SSTANSARD: pysep.io.nml.physics.paramConstruct.SSTANSARDd = SSTANSARDd(SS1=0.9681, SS2=1.0058, SS3=1.0, SS4=0.8966, SS5=1.2727, SS6=0.512, SS7=0.9894, SS8=1.0, SS9=1.0, SS10=1.0, SS11=1.0, SS12=1.0, SS13=1.0, SS14=1.0, SS15=1.0, SS16=0.8642, SS17=0.2875, SS18=1.0, SS19=1.0), WEAKSCREENING: float = 0.03, LDIFAD: int = False, LNOJ: int = False, SENV0A: int = False, ZENV0: float = 0.02, LSTORE: int = False, NPENV: int = 20, NPRTPT: int = 1, NMODLS: int = 1, NBN: float = 1.0, RSCLCM: float = 1.0, ZSI: float = 0.0, HPTTOL: int = 1, XNEWCP: int = 13, LPTIME: bool = True, CMIXL: float = 1.72, BETAC: float = 0.0, LADOV: int = False, LEXCOM: bool = False, LPULSE: int = False, IPVER: int = 2, LDIFY: bool = True, LSNU: bool = True, LTHOULFIT: bool = False, LDH: bool = True, LSEMIC: bool = False, LISO: int = False, LNULOS2: bool = True, LOPALE: bool = False, IAFE: int = 0, LSCV: int = False, LZAMFIT: int = True, LHAFT: bool = True, LOPCOEF: int = False, FO95COBIN: str = '/Users/aaron/dsep/run/OPAL_GS98.bin', LHB: int = False, LFREE_EOS: bool = True, LUSENEWPHX: int = False, LFIFZ: bool = True)¶

Bases: pysep.io.nml.physics.paramConstruct.solar

KTTAU: int = 0¶

LFREE_EOS: bool = True¶

LNEW0: bool = True¶

LOVSTC: bool = False¶

LOVSTE: bool = True¶

class pysep.io.nml.physics.paramConstruct.solar(ATMMIN: float = 0.015, ATMBEG: float = 0.015, ATMERR: float = 1e-05, ATMMAX: float = 0.05, ATMD0: float = 1e-10, ANEWCP: str = ' ', ATMP: str = 'REL', ACFPFT: float = 1e-36, ATIME: pysep.io.nml.physics.paramConstruct.ATIMEd = ATIMEd(minCentralXBeforeHBurning=0.0001, maxChangeXforCoreHBurning=0.02, maxFractionalChangeCentral=0.2, maxChangeYCentral=0.02, maxFractionalChangeYCentral=0.03, maxMassAllowedToBurnInShell=0.0015, maxDepletionInXAtMidpointOfHShell=0.1, maxChangeP=0.02, maxChangeT=0.4, maxChangeR=0.02, maxChangeL=0.02, maxPercentageTimestepChange=0.25, maxFractionalTimestepChange=1.01, maxAbsoluteTimestepChange=- 10000000.0), ALPHAC: float = 0.0, ALPHAE: float = 0.0, ALFA: float = 1.5, ALPHAM: float = 0.0, ATMSTP: float = 0.01, ABSTOL: float = 1e-06, CMIN: float = 1e-20, CLSUN: float = 3.8418e+33, CRSUN: float = 69598000000.0, DPENV: float = 1.0, DTDIF: float = 0.01, DTWIND: float = 10.0, DJOK: float = 0.0001, DT_GS: float = 0.1, ENVERR: float = 1e-05, ENVMAX: float = 0.05, ENVMIN: float = 0.015, ENVBEG: float = 0.015, ENVSTP: float = 0.01, ETADH0: float = - 1.0, ETADH1: float = 1.0, FCORR0: float = 0.8, FCORRI: float = 0.1, FK: float = 1.0, FW: float = 1.0, FC: float = 1.0, FO: float = 1.0, FMU: float = 1.0, FES: float = 1.0, FCORE: float = 1.0, FGSF: float = 1.0, FSS: float = 1.0, FESC: float = 1.0, FSSC: float = 1.0, FGSFC: float = 1.0, FGRY: float = 1.0, FGRZ: float = 1.0, GRTOL: float = 2e-07, HTOLER: pysep.io.nml.physics.paramConstruct.HTOLERd = HTOLERd(convCritDeltaLogP=6e-05, convCritDeltaLogT=4.5e-05, convCritDeltaLLsun=0.003, convCritHeBurning=9e-05, convTolerLogPLogR=3e-05, maxCorrectionDeltaLogP=90000.0, maxCorrectionDeltaLogT=50000.0, maxCorrectionDeltaLLsun=50000.0, maxCorrectionDeltaR=50000000000.0, convTolerRHSofTL=2.5e-06), ITFP1: int = 5, ITFP2: int = 20, IMAX: int = 11, ITDIF1: int = 1, ITDIF2: int = 1, IES: int = 1, IGSF: int = 1, IMU: int = 1, ILAMBDA: int = 4, IEOS: pysep.io.nml.physics.paramConstruct.IEOSd = IEOSd(if1=1, if2=101, if3=0), KTTAU: int = 5, KEMMAX: int = 50, LCOREL: bool = True, LVFC: bool = False, LDIFZ: bool = False, LNEWCP: bool = False, LKUTHE: bool = False, LOVSTC: bool = True, LOVSTE: bool = False, LOVSTM: bool = False, LROT: bool = False, LNEW0: bool = False, LINSTB: bool = False, LWNEW: bool = False, LJDOT0: bool = False, LENVG: bool = False, LNULOS1: bool = True, LTHOUL: bool = False, LCORE: bool = False, LNEWS: bool = True, LISUN: float = 1.45e-11, LSOLID: bool = False, MCORE: int = 1, NITER1: int = 2, NITER2: int = 40, NITER3: int = 0, NITER4: int = 0, NUSE: int = 7, NITER_GS: int = 10, OPTOL: float = 1e-08, OMEGASUN: float = 2.865e-06, RCRIT: float = 1000.0, RELTOL: float = 1e-05, STOLR0: float = 1e-07, SHELLTOL: pysep.io.nml.physics.paramConstruct.SHELLTOLd = SHELLTOLd(minChangeLogM=1e-10, maxChangeLogM=0.05, DeltaXReqToFlag=0.02, DeltaYReqToFlag=1.0, maxDisconX=1.0, maxDisconZ=1.0, dLogPEtxtenBelowOvershootAboveBaseSufraceCZ=0.0, maxdLogPSurfCZAboveFineMeshZone=0.01, maxChangeLLsun=0.01, maxdLogPInFineMeshZone=0.02, maxdLogPBelowSurfCZBelowFineMeshZone=0.02, maxdLogOmega=0.1), TCUT: pysep.io.nml.physics.paramConstruct.TCUTd = TCUTd(lowTempCuttoffAll=6.5, lowTempCuttoffPP=6.5, lowTempCuttoffCNO=6.82, lowTempCuttoffHe=7.73, lowTempCuttoffNuEmission=7.5), TSCUT: float = 6.0, TENV0: float = 3.0, TENV1: float = 9.0, TGCUT: float = 6.9, TRIDT: float = 0.001, TRIDL: float = 8000.0, TOLLFK: float = 0.0001, TOLLFC: float = 0.0001, WALPCZ: float = 0.0, WNEW: float = 0.0, XMIN: float = 0.001, YMIN: float = 0.001, SSTANSARD: pysep.io.nml.physics.paramConstruct.SSTANSARDd = SSTANSARDd(SS1=0.9681, SS2=1.0058, SS3=1.0, SS4=0.8966, SS5=1.2727, SS6=0.512, SS7=0.9894, SS8=1.0, SS9=1.0, SS10=1.0, SS11=1.0, SS12=1.0, SS13=1.0, SS14=1.0, SS15=1.0, SS16=0.8642, SS17=0.2875, SS18=1.0, SS19=1.0), WEAKSCREENING: float = 0.03, LDIFAD: int = False, LNOJ: int = False, SENV0A: int = False, ZENV0: float = 0.02, LSTORE: int = False, NPENV: int = 20, NPRTPT: int = 1, NMODLS: int = 1, NBN: float = 1.0, RSCLCM: float = 1.0, ZSI: float = 0.0, HPTTOL: int = 1, XNEWCP: int = 13, LPTIME: bool = True, CMIXL: float = 1.72, BETAC: float = 0.0, LADOV: int = False, LEXCOM: bool = False, LPULSE: int = False, IPVER: int = 2, LDIFY: bool = True, LSNU: bool = True, LTHOULFIT: bool = False, LDH: bool = True, LSEMIC: bool = False, LISO: int = False, LNULOS2: bool = True, LOPALE: bool = False, IAFE: int = 0, LSCV: int = False, LZAMFIT: int = True, LHAFT: bool = True, LOPCOEF: int = False, FO95COBIN: str = '/Users/aaron/dsep/run/OPAL_GS98.bin', LHB: int = False, LFREE_EOS: bool = False, LUSENEWPHX: int = False, LFIFZ: bool = True)¶

Bases: pysep.io.nml.physics.paramConstruct.base

ABSTOL: float = 1e-06¶

ANEWCP: str = ' '¶

ATIME: pysep.io.nml.physics.paramConstruct.ATIMEd = ATIMEd(minCentralXBeforeHBurning=0.0001, maxChangeXforCoreHBurning=0.02, maxFractionalChangeCentral=0.2, maxChangeYCentral=0.02, maxFractionalChangeYCentral=0.03, maxMassAllowedToBurnInShell=0.0015, maxDepletionInXAtMidpointOfHShell=0.1, maxChangeP=0.02, maxChangeT=0.4, maxChangeR=0.02, maxChangeL=0.02, maxPercentageTimestepChange=0.25, maxFractionalTimestepChange=1.01, maxAbsoluteTimestepChange=-10000000.0)¶

ATMBEG: float = 0.015¶

ATMD0: float = 1e-10¶

ATMERR: float = 1e-05¶

ATMMAX: float = 0.05¶

ATMMIN: float = 0.015¶

ATMP: str = 'REL'¶

ATMSTP: float = 0.01¶

CLSUN: float = 3.8418e+33¶

CMIN: float = 1e-20¶

CRSUN: float = 69598000000.0¶

DPENV: float = 1.0¶

DT_GS: float = 0.1¶

ENVBEG: float = 0.015¶

ENVERR: float = 1e-05¶

ENVMAX: float = 0.05¶

ENVMIN: float = 0.015¶

ENVSTP: float = 0.01¶

ETADH0: float = -1.0¶

ETADH1: float = 1.0¶

FCORE: float = 1.0¶

FCORR0: float = 0.8¶

FCORRI: float = 0.1¶

FGRY: float = 1.0¶

FGRZ: float = 1.0¶

GRTOL: float = 2e-07¶

HTOLER: pysep.io.nml.physics.paramConstruct.HTOLERd = HTOLERd(convCritDeltaLogP=6e-05, convCritDeltaLogT=4.5e-05, convCritDeltaLLsun=0.003, convCritHeBurning=9e-05, convTolerLogPLogR=3e-05, maxCorrectionDeltaLogP=90000.0, maxCorrectionDeltaLogT=50000.0, maxCorrectionDeltaLLsun=50000.0, maxCorrectionDeltaR=50000000000.0, convTolerRHSofTL=2.5e-06)¶

IEOS: pysep.io.nml.physics.paramConstruct.IEOSd = IEOSd(if1=1, if2=101, if3=0)¶

ILAMBDA: int = 4¶

IMAX: int = 11¶

KEMMAX: int = 50¶

KTTAU: int = 5¶

LCORE: bool = False¶

LCOREL: bool = True¶

LDH: bool = True¶

LDIFY: bool = True¶

LENVG: bool = False¶

LEXCOM: bool = False¶

LFIFZ: bool = True¶

LFREE_EOS: bool = False¶

LHAFT: bool = True¶

LNEW0: bool = False¶

LNEWCP: bool = False¶

LNEWS: bool = True¶

LNULOS1: bool = True¶

LNULOS2: bool = True¶

LOPALE: bool = False¶

LOVSTC: bool = True¶

LOVSTE: bool = False¶

LOVSTM: bool = False¶

LPTIME: bool = True¶

LSEMIC: bool = False¶

LSNU: bool = True¶

LTHOULFIT: bool = False¶

MCORE: int = 1¶

NITER1: int = 2¶

NITER2: int = 40¶

NITER3: int = 0¶

NITER4: int = 0¶

NITER_GS: int = 10¶

NUSE: int = 7¶

OPTOL: float = 1e-08¶

RELTOL: float = 1e-05¶

SHELLTOL: pysep.io.nml.physics.paramConstruct.SHELLTOLd = SHELLTOLd(minChangeLogM=1e-10, maxChangeLogM=0.05, DeltaXReqToFlag=0.02, DeltaYReqToFlag=1.0, maxDisconX=1.0, maxDisconZ=1.0, dLogPEtxtenBelowOvershootAboveBaseSufraceCZ=0.0, maxdLogPSurfCZAboveFineMeshZone=0.01, maxChangeLLsun=0.01, maxdLogPInFineMeshZone=0.02, maxdLogPBelowSurfCZBelowFineMeshZone=0.02, maxdLogOmega=0.1)¶

SSTANSARD: pysep.io.nml.physics.paramConstruct.SSTANSARDd = SSTANSARDd(SS1=0.9681, SS2=1.0058, SS3=1.0, SS4=0.8966, SS5=1.2727, SS6=0.512, SS7=0.9894, SS8=1.0, SS9=1.0, SS10=1.0, SS11=1.0, SS12=1.0, SS13=1.0, SS14=1.0, SS15=1.0, SS16=0.8642, SS17=0.2875, SS18=1.0, SS19=1.0)¶

STOLR0: float = 1e-07¶

TENV0: float = 3.0¶

TENV1: float = 9.0¶

TGCUT: float = 6.9¶

TRIDL: float = 8000.0¶

TRIDT: float = 0.001¶

TSCUT: float = 6.0¶

XMIN: float = 0.001¶

XNEWCP: int = 13¶

YMIN: float = 0.001¶

pysep.io.nml.physics.physics module¶

Author: Thomas M. Boudreaux

Created: April 2021

Last Modified: June 2021

Module to handel both dsep run (cards in the control namelist file) as well as the entire control namelist file.

Classes¶

pnml
physics namelist file object. These can be made up of up to 50 crun objects along with a number of attributes not tied into a crun object.

pysep.io.nml.physics.physics.load(path: str) → pysep.io.nml.physics.physics.pnml¶

Load a physics namelist file from disk (note that this loads a fortran physics namelist file into a pnml object, NOT a pickeled pnml object back into memory, for that use pickle.load)

Parameters: path (str) – Path to physics namelist file to load.
Returns: Physics namelist file loaded from disk.
Return type: pysep.io.nml.physics.pnml

class pysep.io.nml.physics.physics.pnml(unit=13, **kwargs)¶

Bases: object

Physics namelist file object representation. This object is the equivilent to the physics namelist file used when running dsep. It can represent all the same information which a physics namelist file representes. Moreover, it can be written to disk in the form of a fortran namelist file so that dsep can read it in. Because it is a python object though it can also be programatically modified and tested.

When writing to disk (for symlinking) pnml will write a namelist file to a temporaty file in /var/tmp and then symbolically link a unit file in the current working directory to that temporary file. Therefore, the actual physics namelist file will be deleted when the pnml instance goes out of scope. To combat this you can explicitly save a namelist representation of the pnml to disk using the save method.

Finally, when pickled, if the pnml has been locally symlinked (and therefore has open a temporary file) that file will be explicitly deleted as file objects cannot be pickled. Therefore you cannot symlink a pnml object, pickle it, load it, and start back where you were. You have to symlink it again after loading the pickle dump.

unit¶

The unit number to symbolically link the control namelist file to.

Type: int, default=14

dsepAttrs¶

Dictionary of all the different attributes which the physics namelist file can store. These are stored as key value pairs with the key being the variale name and the value being the variable value. These are passed to the constructor as an arbitrary number of keyword arguments which will all (aside from unit) become key value pairs in the dsepAttrs dictionary.

Type: dict of control namelist file key value pairs

add_key(key: str, value)¶

Add a new key to physics namelist. If the key is not created then create it if the key is already present raise an error. All keys will be made lowercase to match FORTRANs case insensitivity.

Parameters

key (str) – The name of any class instance attribute which is defined. Case insensitive (will be made lower case automatically).
value – Any data to store in the class instance attribute named key

Returns

Return type

None

Raises

KeyError – If key is already in the kind card

as_dict(generalizePaths=False) → dict¶

Get a dictionary representation of the physics namelist file object

Parameters: generalizePaths (bool, default=False) – This does not do anything, but is included as a function argument to maintain compatibility with pysep.io.nml.control.cnml
Returns: dictRepr – Dictionary representation.
Return type: dict

clean_symlinks()¶: If already locally symlinked then remove the unit file fort.<unit> and set the state of the cnml instance to no longer be locally symlinked.

copy() → pysep.io.nml.physics.physics.pnml¶

Return a deep copy of the pnml object

Returns: newOne – Deep Copy of the parent pnml object.
Return type: pysep.io.nml.physics.pnml

locally_symlink()¶

Symbolically link the physics namelist file to the correct unit file in the current working directory. Instead of saving the pnml file to the current working directory or some user defined path, this function saves the pnml file to a NamedTemporaryFile in /var/tmp (on a linux machine at least). This has the advantage of not cluttering up the local directory as well as automatically deleting the nml file after you send the pnml object out of scope. Once the temporary file has been opned f90nml writes the dicitonary version of the data stored in this object to it. Finally that temporary file is symbolically linked to fort.<unit> in the current working directory.

Because we need to keep the file object in scope as long as we want to be able to access the namelist file, the file object is stored as a class attribute, f.

If a file or symlink called fort.<unit> already exists in the current working directory when this method is called it will be deleted and replaced with the symbolic link created by this method.

Raises: OSError – If the NamedTemporaryFile was unable to be properly opened.

save(path: str) → bool¶

Save pnml file as a fortran namelist file to disk.

Parameters: path (str) – Path to save namelist file to. If path exists already it will be overwritten.
Returns: Check whether namelist file was creates sucessfully. Will be true if file exists and false if it was not able to be creates.
Return type: bool

update_key(key: str, value, overwright: bool = True)¶

update a key in a physics namelist file. By default if the key is already present overwrite it. If the key is not present automatically add it. If overwright is set to false then this will only allow you to add keys (in that case its behavior becomes the same as add_key)

Parameters

key (str) – The name of any class instance attribute which is defined.
value – Any data to store in the class instance attribute named key
overwright (bool, default = True) – if true then if the key already exists overwright it, if false prevent this from happening. If this is true then the old value of the key will be returne from the function. If this is false then None will be returned from the function.

Returns

if overwright is true and the key is in the physics namelist already then the Value which was overwritten will be returned.

Return type

OldValue

pysep.io.nml.physics.utils module¶

Author: Thomas M. Boudreaux

Created: September 2021

Last Modified: September 2021

Utility Functions for converting pnml to dictionary and back

Functions¶

pnml_from_dict
Return a pnml object from a dictionary.

pysep.io.nml.physics.utils.pnml_from_dict(params: dict) → pysep.io.nml.physics.physics.pnml¶

Return a cnml object from a dictionary.

Parameters: params (dict) – Dictionary containing all the required information to rebuild the cnml object, including a list of all the crun dictionaries.
Returns: outCnml – cnml object
Return type: pysep.io.nml.physics.physics.cnml

pysep.io.nml.physics package¶

Subpackages¶

Submodules¶

pysep.io.nml.physics.paramConstruct module¶

pysep.io.nml.physics.physics module¶

Classes¶

pysep.io.nml.physics.utils module¶

Functions¶

Module contents¶