if self.objPyxb !=None : self.objPyxb.objAccas=self
#print ('X_MCSIMP', self.nom, self.objPyxb, )
- print ('fin X_MCSIMP', self.objPyxb, self.nom, self, self.maClasseModeleMetier,self.valeur)
+ #print ('fin X_MCSIMP', self.objPyxb, self.nom, self, self.maClasseModeleMetier,self.valeur)
def setValeurObjPyxb(self,newVal):
from cata_Vimmp import *
+#Ajouter Qlqs retours chariots
+#Documentation :
+nstlist_ang=">0\n\tFrequency to update the neighbor list (and the long-range forces, when using twin-range cut-offs). When this is 0, the neighbor list is made only once. With energy minimization the neighborlist will be updated for every energy evaluation when nstlist>0. With cutoff-scheme=Verlet and verlet-buffer-tolerance set, nstlist is actually a minimum value and mdrun might increase it, unless it is set to 1. With parallel simulations and/or non-bonded force calculation on the GPU, a value of 20 or 40 often gives the best performance. With cutoff-scheme=Group and non-exact cut-off's, nstlist will affect the accuracy of your simulation and it can not be chosen freely.\n0\n\tThe neighbor list is only constructed once and never updated. This is mainly useful for vacuum simulations in which all particles see each other.\n-1\n\tAutomated update frequency, only supported with cutoff-scheme=group. This can only be used with switched, shifted or user potentials where the cut-off can be smaller than rlist. One then has a buffer of size rlist minus the longest cut-off. The neighbor list is only updated when one or more particles have moved further than half the buffer size from the center of geometry of their charge group as determined at the previous neighbor search. Coordinate scaling due to pressure coupling or the deform option is taken into account. This option guarantees that their are no cut-off artifacts, but for larger systems this can come at a high computational cost, since the neighbor list update frequency will be determined by just one or two particles moving slightly beyond the half buffer length (which does not necessarily imply that the neighbor list is invalid), while 99.99% of the particles are fine. \n"
+
+
#CodeSpecific=OPER(nom='CodeSpecific', sd_prod = SPM_SD,
CodeSpecific=PROC(nom='CodeSpecific',
# Gromacs_Physical_Description = FACT(statut='o',
# ), # Gromacs_Physical_Description
-
-
+
Gromacs_Numerical_Description = FACT(statut='o',
Integrator = SIMP(statut='o',typ='TXM', into=['steep','md'] ),
b_steep = BLOC(condition = " Integrator == 'steep'",
Gromacs_Neighbor_Searching = FACT(statut = 'o',
cutoff_scheme = SIMP(statut='o', typ ='TXM', into = ['verlet','group'],),
#TODO : Analyser plus en details les valeurs par defaut possibles pour ce parametre
- nstlist = SIMP(statut ='o', typ='I', defaut=10),
+ #TODO : En particulier si ==0 annihiler les cut-offs
+ nstlist = SIMP(statut ='o', typ='I', defaut=10, ang=nstlist_ang),
nst_type = SIMP(statut ='o', typ='TXM', into=['grid','simple'], defaut='grid'),
Consigne = SIMP(statut='o',typ='TXM',homo='information',defaut='pbc parameter comes from the common data model'),
#TODO : la relation a pbc n'est pas clair ds la doc
+ #L'activation de periodic_molecules a faire uniquement si cdm.Boundary_Conditions.Type_Of_Boundary_Condition == periodic
periodic_molecules = SIMP(statut ='o', typ=bool),
- b_rlist = BLOC(condition = "cutoff_scheme == 'group'",
+ # b_rlist = BLOC(condition = "cutoff_scheme == 'group'",
rlist = SIMP(statut ='o', typ='I', defaut=-1,ang="[nm]"),
- ),
+ # ),
rcoulomb = SIMP(statut ='o', typ='R', defaut=1, val_min=0,ang="[nm] distance for the Coulomb cut-off"),
rvdw = SIMP(statut ='o', typ='R', defaut=1, val_min=0,ang="[nm] distance for the LJ or Buckingham cut-off"),
),
rcoulomb=1.0,
rvdw=1.0,),
Gromacs_Run_Options=_F(UserDef='-DFLEX_SRC',
- Files=_F(MDP_Initial_Input_File='/tmp/pp',
- Gromos_File=\
+ Files=_F(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',),),);
+ log_File='/tmp/EM.log',
+ MDP_Initial_Input_File='/tmp/pp',),),);
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,
+ Nb_Of_Steps=100000,
nstcomm=1,),
- Gromacs_Neighbor_Searching=_F(cutoff_scheme='group',
+ Gromacs_Neighbor_Searching=_F(cutoff_scheme='verlet',
nstlist=10,
nst_type='grid',
periodic_molecules=True,
- rlist=-1,
+ rlist=1,
rcoulomb=1.0,
rvdw=1.0,),
- Gromacs_Run_Options=_F(Files=_F(MDP_Initial_Input_File='/tmp/pp',
- Gromos_File=\
+ Gromacs_Initial_Conditions=_F(gen_vel='yes',
+ gen_temp=300.0,
+ gen_seed=-1.0,),
+ Gromacs_Run_Options=_F(Files=_F(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',),),);
-#CHECKSUM:3a12a89edafb2f537cf149f58ce44d9c -:FIN CHECKSUM
\ No newline at end of file
+ MDP_File='nvt.mdp',
+ Run_Input_File='CNT53_12x057_nvt.trr',
+ log_File='/tmp/nvt.log',
+ MDP_Initial_Input_File=\
+ '/home/C65845/VIMMP/vimmp.training/app/session10/datafiles/nvt_initial.mdp',),),);
+#CHECKSUM:b39984f8d550e349da6b357927ed35f6 -:FIN CHECKSUM
\ No newline at end of file
