From a5b4e2f1021630d3e100ca33cbccc83b118427da Mon Sep 17 00:00:00 2001 From: Eric Fayolle Date: Tue, 7 May 2019 19:41:32 +0200 Subject: [PATCH] =?utf8?q?Am=C3=A9lioration=20du=20cata=5Fvimmp=20+=20cata?= =?utf8?q?=5Fgromacs?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- Vimmp/Makefile | 7 +++++++ Vimmp/cata_Vimmp.py | 23 +++++++++-------------- Vimmp/cata_gromacs.py | 20 +++++++++++++------- Vimmp/gromacs_em+nvt_v1.comm | 8 ++++---- 4 files changed, 33 insertions(+), 25 deletions(-) diff --git a/Vimmp/Makefile b/Vimmp/Makefile index c712b251..53d500a5 100644 --- a/Vimmp/Makefile +++ b/Vimmp/Makefile @@ -7,6 +7,13 @@ PYXB_PYTHONPATH=/local/PyXB-1.2.6.bin/lib/python2.7/site-packages/ # L'utilisation de $? ne fonctionne pas s'il on modifie qu'un catalogue car il ne redonne pas le fichier non modifier et pyxb détecte # que l'autre fichier en dépend et n'est pas regénéré : $^ + +cata_Vimmp_genere.py: cata_Vimmp.py + generateXSD.py -c ./$< + +cata_gromacs_genere.py: cata_gromacs.py + generateXSD.py -c ./$< + all: cata_Vimmp_genere.py cata_gromacs_genere.py cata_Vimmp_genere.py: cata_Vimmp_genere.xsd diff --git a/Vimmp/cata_Vimmp.py b/Vimmp/cata_Vimmp.py index 15015dd9..53d6b27d 100644 --- a/Vimmp/cata_Vimmp.py +++ b/Vimmp/cata_Vimmp.py @@ -229,27 +229,22 @@ CDM = OPER(nom = 'CDM', sd_prod = CDM_SD, ),# fin bloc_elec bloc_VdW = BLOC( condition = 'Type_Of_Unbonded_Interaction == "Repulsion_and_VdW"', - type_Repulsion_and_VdW = SIMP( statut='o', typ='TXM', into = [ 'Lennard_Jones', 'Hard_sphere_model'], position='global' ), - ), # fin bloc_VdW - - bloc_not_elec = BLOC( condition = 'Type_Of_Unbonded_Interaction not in( "electro_magnetic", "No") ', - Species_Pair_Parameters = FACT( statut='o', max="**", + Species_Pair_Parameters = FACT( statut='o', max="**", + Type_Repulsion_and_VdW = SIMP( statut='o', typ='TXM', into = [ 'Lennard_Jones', 'Hard_sphere_model']), Species_Pair = SIMP( statut='o', max=2, typ='TXM'), - b_Param_Potential_Type_LJ_1 = BLOC( condition = "Type_Of_Unbonded_Interaction == 'Repulsion_and_VdW'", - VdW_Radius = SIMP( statut='o', typ='R', val_min=0), - b_PPal_LJ2 = BLOC( condition = "type_Repulsion_and_VdW == 'Lennard_Jones'", + VdW_Radius = SIMP( statut='o', typ='R', val_min=0), + b_Lennard = BLOC( condition = "Type_Repulsion_and_VdW == 'Lennard_Jones'", Depth_Of_The_Potential_Well = SIMP( statut='o', typ='R', val_min=0), - ), # fin b_b_PPal_LJ2 - ), # fin b_Param_Potential_Type_LJ_1 + ), # fin b_Lennard + ), # fin Species_Pair_Parameters + ), # bloc_VdW - b_Param_Soft_Potentiel = BLOC( condition = "Type_Of_Unbonded_Interaction == 'Soft_Potentiel'", + b_Param_Soft_Potentiel = BLOC( condition = "Type_Of_Unbonded_Interaction == 'Soft_Potentiel'", Groot_Warren_Repulsion = SIMP( statut='o', typ='R', defaut=25.0, val_min=0), Groot_Warren_Cutoff = SIMP( statut='o', typ='R', defaut=1.0, val_min=0), Drag_Coefficient = SIMP( statut='o', typ='R'), # les 2 valent 0 pour MD Drag_Force_Cutoff = SIMP( statut='o', typ='R', val_min=0), - ), # b_Param_Soft_Potentiel - ), # Species_Pair_Parameters - ),# fin bloc_not_elec + ), # b_Param_Soft_Potentiel ), # fin UnBonded_Interactions diff --git a/Vimmp/cata_gromacs.py b/Vimmp/cata_gromacs.py index e59446bd..5214c678 100644 --- a/Vimmp/cata_gromacs.py +++ b/Vimmp/cata_gromacs.py @@ -4,11 +4,6 @@ from cata_Vimmp import * CodeSpecific=PROC(nom='CodeSpecific', # Gromacs_Physical_Description = FACT(statut='o', - gen_vel = SIMP(statut='o', typ = bool, defaut = False), - b_Velocity_Generation = BLOC(condition = "gen_vel == True", - 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_Physical_Constraints = FACT(statut = 'o', # pour Gromacs, rien = linear @@ -97,11 +92,20 @@ CodeSpecific=PROC(nom='CodeSpecific', ), 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"), - ), + ), + + 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", + 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_Initial_Conditions + 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='o', typ = ('FichierNoAbs','mdp Files (*.mdp);;All Files (*)')), + MDP_Initial_Input_File = SIMP(statut='f', typ = ('FichierNoAbs','mdp Files (*.mdp);;All Files (*)')), 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 (*)')), @@ -114,5 +118,7 @@ CodeSpecific=PROC(nom='CodeSpecific', ), # Files_Energy_Minimization ), # Gromacs_Run_Options + + ) diff --git a/Vimmp/gromacs_em+nvt_v1.comm b/Vimmp/gromacs_em+nvt_v1.comm index 6c1c09b4..a55b7002 100644 --- a/Vimmp/gromacs_em+nvt_v1.comm +++ b/Vimmp/gromacs_em+nvt_v1.comm @@ -35,11 +35,11 @@ NanoTube12=CDM(Title='NanoTubeC53', Mean_Bond_Length=4.0,),),), Unbonded_Interactions=_F( Type_Of_Unbonded_Interaction='Repulsion_and_VdW', - type_Repulsion_and_VdW='Lennard_Jones', Species_Pair_Parameters=_F( + Type_Repulsion_and_VdW='Lennard_Jones', Species_Pair=('C','C',), - VdW_Radius=0.355, - Depth_Of_The_Potential_Well=0.292288,),), + VdW_Radius=0.355e-01, + Depth_Of_The_Potential_Well=2.92288e-01,),), External_Field_Interaction=_F( Type_Of_Interaction_With_An_External_Field='No',),), Statistical_Physics=_F(Type_Of_Statistical_Physics=\ @@ -79,4 +79,4 @@ CodeSpecific(gen_vel=False, MDP_File='em.mdp', Run_Input_File='CNT53_12x057_em.trr', log_File='/tmp/EM.log',),),); -#CHECKSUM:36af6eab259960058e9e5820059cf926 -:FIN CHECKSUM \ No newline at end of file +#CHECKSUM:de076b75bd06fb1d8435eb83bdcfbe4f -:FIN CHECKSUM \ No newline at end of file -- 2.39.2