Amélioration du cata_vimmp + cata_gromacs

diff --git a/Vimmp/Makefile b/Vimmp/Makefile
index c712b2516661d4043004a091f3a811b7bcfc8fed..53d500a5cbe16a0ed39b990da3a9fb193ba646e9 100644 (file)
--- 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 15015dd92890bb5071a47969012c2782e0b9b01d..53d6b27db31bc42110d67c122f193b6d06f8fc89 100644 (file)
--- 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 e59446bdade01ba65626e7b904c459834ed359e1..5214c678c16700778d56940d47d4ddeb06c28230 100644 (file)
--- 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 6c1c09b454799d71c37bc1dc54467dd76dc40728..a55b7002ca348f0bbf979ccf66ad28a746ae7736 100644 (file)
--- 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