if self.objPyxb : self.objPyxb.objAccas=self
#print ('X_MCSIMP', self.nom, self.objPyxb, )
- #print ('fin X_MCSIMP', self.objPyxb, self.nom,self)
+ #print ('fin X_MCSIMP', self.objPyxb, self.nom,self, self.maClasseModeleMetier,self.valeur)
def setValeurObjPyxb(self,newVal):
# -------------------------
#
def buildObjPyxb(self,mc_list) :
- #print ('________________________________________________')
+ print ('________________________________________________')
if not self.cata.modeleMetier : return
- #print ('X_MCCOMPO buildObjPyxb', self, mc_list)
+ print ('X_MCCOMPO buildObjPyxb', self, mc_list)
self.listArg=[]
+ dicoargs={}
for objAccas in mc_list :
if objAccas.nature == 'MCBLOC' :
self.exploreBLOC(objAccas)
elif objAccas.nature == 'MCList' :
for fils in objAccas :
- #print (fils.nom)
+ # print (fils.nom)
+ # print (fils.objPyxb,fils.maClasseModeleMetier)
fils.perePyxb=self
self.listArg.append(fils.objPyxb)
+ dicoargs[fils.nom]=fils.objPyxb
else :
+ #print (objAccas.nom,objAccas.maClasseModeleMetier)
if objAccas.nom == 'Consigne' : continue
self.listArg.append(objAccas.objPyxb)
+ dicoargs[objAccas.nom]=objAccas.objPyxb
objAccas.perePyxb=self
+ print('X_MCCOMPO -- listArg ---',self.nom,self.listArg)
+
self.monNomClasseModeleMetier='T_'+self.nom
if self.nom in list(self.cata.DicoNomTypeDifferentNomElt.keys()) :
self.monNomClasseModeleMetier=self.cata.DicoNomTypeDifferentNomElt[self.nom][self.nomComplet()]
self.maClasseModeleMetier=getattr(self.cata.modeleMetier,self.monNomClasseModeleMetier)
+
if self.objPyxbDeConstruction != None :
self.objPyxb = self.objPyxbDeConstruction
self.objPyxbDeConstruction = None
else :
#print (self.nom)
#print (self.listArg)
- self.objPyxb=self.maClasseModeleMetier(*self.listArg)
+ # self.objPyxb=self.maClasseModeleMetier(*self.listArg)
+ self.objPyxb=self.maClasseModeleMetier(**dicoargs)
+ newordercontent=[]
+ for obj in self.listArg:
+ print('X_MCCOMPO -- obj ----',obj)
+ newordercontent.append( self.objPyxb.orderedContent()[map(lambda o:id(o.value), self.objPyxb.orderedContent()).index(id(obj))] )
+
+ for i in xrange(len(self.listArg)):
+ self.objPyxb.orderedContent()[i]=newordercontent[i]
self.objPyxb.objAccas=self
- #print ('X_MCCOMPO', self, self.nom, self.objPyxb)
- #print ('_______________________________________')
+ print ('X_MCCOMPO', self, self.nom, self.objPyxb,self.listArg,newordercontent,self.objPyxb.orderedContent())
+ print ('_______________________________________')
+ # assert(self.objPyxb.validateBinding())
def delObjPyxb(self):
if not self.cata.modeleMetier : return
# print(e.details())
def toXml(self,fichier=None):
- #print ('ds to XML')
+ print ('ds to XML')
if not self.cata.modeleMetier : return
- #print ('***************',self.objPyxb,'***************',)
- #print ('***************',self,'***************',)
- #print ('***************',self.objPyxb.orderedContent(),'***************',)
- #print(self.objPyxb.toDOM().toprettyxml())
- #print(self.objPyxb.toxml())
+ print ('***************',self.objPyxb,'***************',)
+ print ('***************',self,'***************',)
+ print ('***************',self.objPyxb.orderedContent(),'***************',)
+ print(self.objPyxb.toDOM().toprettyxml())
+ print(self.objPyxb.toxml())
return (self.objPyxb.toDOM().toprettyxml())
Gromacs_Physical_Constraints = FACT(statut = 'o',
# pour Gromacs, rien = linear
- Remove_Center_Of_Mass_Motion = SIMP(statut='o', typ ='TXM', into =['Linear', 'Angular', 'Non Activ'], defaut = 'Non Activ'),
+ Remove_Center_Of_Mass_Motion = SIMP(statut='o', typ ='TXM', into =['Linear', 'Angular', 'Non Activ'], position='global', defaut = 'Non Activ'),
b_recalage_cgt = BLOC (condition = "Remove_Center_Of_Mass_Motion != 'Non Activ'",
Apply_On_The_Complete_System = SIMP ( statut ='o', typ = bool, defaut = True),
b_porte_sur_tout_le_system = BLOC( condition = 'Apply_On_The_Complete_System == False ',
),# b_recalage_cgt
Bond_Constraints = FACT(statut = 'o',
- Bond_Constraint_Type = SIMP(statut='o', typ ='TXM', into =['BC_none', 'h-bonds', 'all-bonds', 'h-angles', 'all-angles'], defaut = 'BC_none'),
+ Bond_Constraint_Type = SIMP(statut='o', typ ='TXM', into =['BC_none', 'h-bonds', 'all-bonds', 'h-angles', 'all-angles'], defaut = 'BC_none',ang="none\n\tNo constraints except for those defined explicitly in the topology, i.e. bonds are represented by a harmonic (or other) potential or a Morse potential (depending on the setting of morse) and angles by a harmonic (or other) potential.\nh-bonds\n\tConvert the bonds with H-atoms to constraints.\nall-bonds\n\tConvert all bonds to constraints.\nh-angles\n\tConvert all bonds and additionally the angles that involve H-atoms to bond-constraints.\nall-angles\n\tConvert all bonds and angles to bond-constraints.\n"),
# We decided not to use < defaut = 'LINCS' > to avoid displaying the conditional block whithout
# displaying the value of Bond_Constraint_Algorithm
Bond_Constraint_Algorithm = SIMP(statut='f', typ ='TXM', into =['LINCS', 'SHAKE'], sug = 'LINCS'),
b_t_coupling_num = BLOC(condition = "tcoupl != 'Non Activ'",
nsttcouple = SIMP(statut ='o', typ='I', defaut=-1),
),
+ b_t_rcmm = BLOC(condition = "Remove_Center_Of_Mass_Motion != 'Non Activ'",
+ nstcomm = SIMP(statut ='o', typ='I', defaut=100,ang="frequency for center of mass motion removal"),
+ ),
),
Gromacs_Neighbor_Searching = FACT(statut = 'o',
cutoff_scheme = SIMP(statut='o', typ ='TXM', into = ['verlet','group'],),
Gromacs_Initial_Conditions = FACT(statut='f',
gen_vel = SIMP(statut='o', typ = 'TXM', into=['yes','no'], defaut = 'yes'),
- b_Velocity_Generation = BLOC(condition = "gen_vel == yes",
+ b_Velocity_Generation = BLOC(condition = "gen_vel == 'yes'",
gen_temp = SIMP(statut='o', typ='R', ang='temperature for Maxwell distribution'),
gen_seed = SIMP(statut='o', typ='R', ang='used to initialize random generator,when -1 a pseudo random seed is used', defaut = -1),
),
Gromacs_Run_Options = FACT(statut='o',
UserDef=SIMP(statut='f', typ='TXM', into=['-DFLEX_SRC',]),
- Files_Energy_Minimization = FACT(statut='o',
- MDP_Initial_Input_File = SIMP(statut='f', typ = ('FichierNoAbs','mdp Files (*.mdp);;All Files (*)')),
+ Files = FACT(statut='o',
Gromos_File = SIMP(statut='o', typ = ('Fichier','gro Files (*.gro);;All Files (*)')),
# en entree de grompp et de mdrun option -c
Gromacs_Topology_File = SIMP(statut='o', typ = ('Fichier','Top Files (*.top);;All Files (*)')),
Run_Input_File = SIMP(statut='o', typ = ('FichierNoAbs')), # doit finir par tpr
log_File = SIMP(statut='f', defaut ='/tmp/EM.log', typ=('FichierNoAbs')),
Energie_Output_File = SIMP(statut='f', typ = ('FichierNoAbs')), # doit finir par edr
+ MDP_Initial_Input_File = SIMP(statut='f', typ = ('FichierNoAbs','mdp Files (*.mdp);;All Files (*)')),
Trajectory_Output_File = SIMP(statut='f', typ = ('FichierNoAbs')), # doit finir par trr
), # Files_Energy_Minimization
-NanoTube12=CDM(Title='NanoTubeC53',
- Simulated_Time_Lapse=_F(Initial_Time=0.0,
- Duration=100.0,),
- Geometric_Domain=_F(Shape='Simplified Shape',
- Box='Cube',
- Size_Of_Bounding_Box=(16.0,16.0,16.0),
- Surface=('INT1','INT52',),),
- System_Component=_F(General_Level_Of_Description='Mesoscopic',
- Component='Classical_Particle System',
- Physical_Description_Particle=_F(List_Of_Species=_F(Number_Of_Species=1,
- Specie=_F(Name_Of_Specie='C',
- Mass_Molaire=12.011,
- Number_of_Particle=784,),),
- List_Of_Bonded_Particles=_F(Bonded_Particles=(_F(
+NanoTube12_EM=CDM(Title='(NanoTubeC53) Energy minimization ',
+ Simulated_Time_Lapse=_F(Initial_Time=0.0,
+ Duration=100.0,),
+ Geometric_Domain=_F(Shape='Simplified Shape',
+ Box='Cube',
+ Size_Of_Bounding_Box=(16.0,16.0,16.0),
+ Surface=('INT1','INT52',),),
+ System_Component=_F(General_Level_Of_Description='Mesoscopic',
+ Component='Classical_Particle System',
+ Physical_Description_Particle=_F(List_Of_Species=_F(Number_Of_Species=1,
+ Specie=_F(Name_Of_Specie='C',
+ Mass_Molaire=12.011,
+ Number_of_Particle=784,),),
+ List_Of_Bonded_Particles=_F(Bonded_Particles=(_F(
Name_Of_Bonded_Particles='C1',
Species_in_Particle=('C','C',),),
- _F(
+ _F(
Name_Of_Bonded_Particles='C2',
Species_in_Particle=('C','C','C',),),
- _F(
+ _F(
Name_Of_Bonded_Particles='C3',
Species_in_Particle=('C','C','C','C',),),),),
- List_Of_Interactions=_F(Bonded_Interactions=(_F(
+ List_Of_Interactions=_F(Bonded_Interactions=(_F(
Type_Of_Bonded_Interaction='Covalent Bond Angle',
- Interaction_Angles_Parameters=_F(
+ Interaction_Angles_Parameters=_F(
Apply_To_Bonded_Particles=('C3','C3',),
Spring_Stifness=1.0,
Mean_Bond_Angle=2.0,),),
- _F(
+ _F(
Type_Of_Bonded_Interaction='Covalent Bond Length',
- Interaction_Length_Parameters=_F(
+ Interaction_Length_Parameters=_F(
Apply_To_Bonded_Particles=('C2',),
Spring_Stifness=3.0,
Mean_Bond_Length=4.0,),),),
- Unbonded_Interactions=_F(
+ Unbonded_Interactions=_F(
Type_Of_Unbonded_Interaction='Repulsion_and_VdW',
- Species_Pair_Parameters=_F(
+ Species_Pair_Parameters=_F(
Type_Repulsion_and_VdW='Lennard_Jones',
Species_Pair=('C','C',),
- VdW_Radius=0.355e-01,
- Depth_Of_The_Potential_Well=2.92288e-01,),),
- External_Field_Interaction=_F(
+ VdW_Radius=0.0355,
+ Depth_Of_The_Potential_Well=0.292288,),),
+ External_Field_Interaction=_F(
Type_Of_Interaction_With_An_External_Field='No',),),
- Statistical_Physics=_F(Type_Of_Statistical_Physics=\
+ Statistical_Physics=_F(Type_Of_Statistical_Physics='No',),),
+ Particle_Representation=_F(Representation_Type='Particle_Representation',
+ Type_Of_Entity='Atom',
+ Numerical_Particle_Model=_F(Type_Of_State_Vector='Kinetic',),
+ Definition_Numerical_Model=_F(Numerical_Model='MD',
+ Structure_Of_The_Evolution_Law=\
+ 'Newton equations',),),),
+ Boundary_Conditions=_F(Type_Of_Boundary_Condition='Periodic',
+ Direction='XYZ',),);
+
+NanoTube12_TE=CDM(Title='(NanoTubeC53) Thermal Equilibrium',
+ Simulated_Time_Lapse=_F(Initial_Time=0.0,
+ Duration=100.0,),
+ Geometric_Domain=_F(Shape='Simplified Shape',
+ Box='Cube',
+ Size_Of_Bounding_Box=(16.0,16.0,16.0),
+ Surface=('INT1','INT52',),),
+ System_Component=_F(General_Level_Of_Description='Mesoscopic',
+ Component='Classical_Particle System',
+ Physical_Description_Particle=_F(List_Of_Species=_F(Number_Of_Species=1,
+ Specie=_F(Name_Of_Specie='C',
+ Mass_Molaire=12.011,
+ Number_of_Particle=784,),),
+ List_Of_Bonded_Particles=_F(Bonded_Particles=(_F(
+ Name_Of_Bonded_Particles='C1',
+ Species_in_Particle=('C','C',),),
+ _F(
+ Name_Of_Bonded_Particles='C2',
+ Species_in_Particle=('C','C','C',),),
+ _F(
+ Name_Of_Bonded_Particles='C3',
+ Species_in_Particle=('C','C','C','C',),),),),
+ List_Of_Interactions=_F(Bonded_Interactions=(_F(
+ Type_Of_Bonded_Interaction='Covalent Bond Angle',
+ Interaction_Angles_Parameters=_F(
+ Apply_To_Bonded_Particles=('C3','C3',),
+ Spring_Stifness=1.0,
+ Mean_Bond_Angle=2.0,),),
+ _F(
+ Type_Of_Bonded_Interaction='Covalent Bond Length',
+ Interaction_Length_Parameters=_F(
+ Apply_To_Bonded_Particles=('C2',),
+ Spring_Stifness=3.0,
+ Mean_Bond_Length=4.0,),),),
+ Unbonded_Interactions=_F(
+ Type_Of_Unbonded_Interaction='Repulsion_and_VdW',
+ Species_Pair_Parameters=_F(
+ Type_Repulsion_and_VdW='Lennard_Jones',
+ Species_Pair=('C','C',),
+ VdW_Radius=0.0355,
+ Depth_Of_The_Potential_Well=0.292288,),),
+ External_Field_Interaction=_F(
+ Type_Of_Interaction_With_An_External_Field='No',),),
+ Statistical_Physics=_F(Type_Of_Statistical_Physics=\
'Equilibrium',
- Distribution='nvt',
- Target_Temperature=300.0,),),
- Particle_Representation=_F(Representation_Type='Particle_Representation',
- Type_Of_Entity='Atom',
- Numerical_Particle_Model=_F(Type_Of_State_Vector='Kinetic',),
- Definition_Numerical_Model=_F(Numerical_Model='MD',
- Structure_Of_The_Evolution_Law=\
+ Distribution='nvt',
+ Target_Temperature=300.0,),),
+ Particle_Representation=_F(Representation_Type='Particle_Representation',
+ Type_Of_Entity='Grain',
+ Numerical_Particle_Model=_F(Type_Of_State_Vector='Kinetic',),
+ Definition_Numerical_Model=_F(Numerical_Model='MD',
+ Structure_Of_The_Evolution_Law=\
'Newton equations',),),),
- Boundary_Conditions=_F(Type_Of_Boundary_Condition='Periodic',
- Direction='XYZ',),);
+ Boundary_Conditions=_F(Type_Of_Boundary_Condition='Periodic',
+ Direction='XYZ',),);
-CodeSpecific(gen_vel=False,
- Gromacs_Physical_Constraints=_F(Remove_Center_Of_Mass_Motion='Non Activ',
+CodeSpecific(Gromacs_Physical_Constraints=_F(Remove_Center_Of_Mass_Motion='Non Activ',
Bond_Constraints=_F(Bond_Constraint_Type='BC_none',),
Temperature_Coupling=_F(tcoupl='Non Activ',),),
Gromacs_Numerical_Description=_F(Integrator='steep',
rcoulomb=1.0,
rvdw=1.0,),
Gromacs_Run_Options=_F(UserDef='-DFLEX_SRC',
- Files_Energy_Minimization=_F(MDP_Initial_Input_File='/tmp/pp',
- Gromos_File=\
+ Files=_F(MDP_Initial_Input_File='/tmp/pp',
+ Gromos_File=\
+ '/home/C65845/VIMMP/vimmp.training/app/gromacs/gromax.testdata/CNT53_12x057.gro',
+ Gromacs_Topology_File=\
+ '/home/C65845/VIMMP/Salome_POLITO_gromacs/GROMACS/CNTconductivity_files/1-EM/TEST/CNT53_12x057.top',
+ MDP_File='em.mdp',
+ Run_Input_File='CNT53_12x057_em.trr',
+ log_File='/tmp/EM.log',),),);
+
+CodeSpecific(Gromacs_Physical_Constraints=_F(Remove_Center_Of_Mass_Motion='Linear',
+ Apply_On_The_Complete_System=True,
+ Bond_Constraints=_F(Bond_Constraint_Type='BC_none',),
+ Temperature_Coupling=_F(tcoupl='Non Activ',),),
+ Gromacs_Numerical_Description=_F(Integrator='md',
+ Nb_Of_Steps=5000,
+ nstcomm=1,),
+ Gromacs_Neighbor_Searching=_F(cutoff_scheme='group',
+ nstlist=10,
+ nst_type='grid',
+ periodic_molecules=True,
+ rlist=-1,
+ rcoulomb=1.0,
+ rvdw=1.0,),
+ Gromacs_Run_Options=_F(Files=_F(MDP_Initial_Input_File='/tmp/pp',
+ Gromos_File=\
'/home/C65845/VIMMP/vimmp.training/app/gromacs/gromax.testdata/CNT53_12x057.gro',
- Gromacs_Topology_File=\
+ Gromacs_Topology_File=\
'/home/C65845/VIMMP/Salome_POLITO_gromacs/GROMACS/CNTconductivity_files/1-EM/TEST/CNT53_12x057.top',
- MDP_File='em.mdp',
- Run_Input_File='CNT53_12x057_em.trr',
- log_File='/tmp/EM.log',),),);
-#CHECKSUM:de076b75bd06fb1d8435eb83bdcfbe4f -:FIN CHECKSUM
\ No newline at end of file
+ MDP_File='em.mdp',
+ Run_Input_File='CNT53_12x057_em.trr',
+ log_File='/tmp/EM.log',),),);
+#CHECKSUM:3a12a89edafb2f537cf149f58ce44d9c -:FIN CHECKSUM
\ No newline at end of file
