bug fix with masses

Src/global_variables.f90

@@ -26,7 +26,7 @@ module global_variables
      integer :: atomtype
      integer :: molid,mer_index,atom_mer_index
      integer :: index
-     real*8 :: charge
+     real*8 :: charge,mass
      real*8 ,dimension(3) :: coord
     end type
     type(allatoms) , dimension(:),allocatable :: printedatoms

Src/print_files.f90

@@ -186,6 +186,12 @@ module print_files
 &           printedatoms(i)%charge,printedatoms(i)%coord
     end do
 
+    write(9,*) 
+    write(9,*) ' Masses'
+    write(9,*) 
+    do i=1,n_atoms
+      write(9,*) i,printedatoms(i)%mass
+    end do
     write(9,*) 
     write(9,*) ' Bonds'
     write(9,*) 
@@ -231,7 +237,7 @@ module print_files
       if ( .not. bonded) then
           print*,iatom,jatom
             print*,'iatom bonds : ',bonds(iatom,:)
-     pause
+    ! pause
       end if
      iostat=0
 
@@ -453,6 +459,7 @@ end if
           printedatoms(cnt)%atomtype=blocks(i)%atype(j)
           printedatoms(cnt)%coord=blocks(i)%coord(j,:)
           printedatoms(cnt)%molid=i
+          printedatoms(cnt)%mass=blocks(i)%mass(j)
           printedatoms(cnt)%index=cnt
 
         end if
@@ -481,6 +488,7 @@ end if
             printedatoms(cnt)%charge=chains(i)%mers(j)%charge(k)
             printedatoms(cnt)%coord=chains(i)%mers(j)%coord(k,:)
             printedatoms(cnt)%molid=n_boxes+i
+            printedatoms(cnt)%mass=chains(i)%mers(j)%mass(k)
             printedatoms(cnt)%index=cnt
             printedatoms(cnt)%mer_index = j
             printedatoms(cnt)%atom_mer_index = k
@@ -501,6 +509,7 @@ end if
         write(146,*) 'H  ',chains(i)%head(:)
         write(147,205)'HETATM',cnt,'H  ','','','',chains(i)%head(:),'H  ',0,0,0.0
             printedatoms(cnt)%symbol='H ' 
+            printedatoms(cnt)%mass=1.0
             printedatoms(cnt)%atomtype=base_mers(chains(i)%mer_id)%htype
             printedatoms(cnt)%charge=base_mers(chains(i)%mer_id)%headcharge
             printedatoms(cnt)%coord=chains(i)%head(:)
@@ -521,6 +530,7 @@ end if
             printedatoms(cnt)%charge=base_mers(chains(i)%mer_id)%tailcharge
             printedatoms(cnt)%coord=chains(i)%tail(:)
             printedatoms(cnt)%molid=n_boxes+i
+            printedatoms(cnt)%mass=1.0
             printedatoms(cnt)%index=cnt
         chains(i)%tailh_atom_index = cnt
         

Test/POSCAR

+24  # number of Atoms
+1.0
+5.041400 0.000000 0.000000
+0.000000 8.792439 0.000000
+0.000000 0.000000 8.776380
+Direct 
+ 1 0.063427 0.824781 0.180519  0 Si 28.08
+ 2 0.936573 0.175219 0.819481  0 Si 28.08
+ 3 0.936573 0.175219 0.180519  0 Si 28.08
+ 4 0.063427 0.824781 0.819481  0 Si 28.08
+ 5 0.563427 0.675219 0.319481  0 Si 28.08
+ 6 0.436573 0.324781 0.680519  0 Si 28.08
+ 7 0.436573 0.324781 0.319481  0 Si 28.08
+ 8 0.563427 0.675219 0.680519  0 Si 28.08
+ 9 0.129253 0.289031 0.276156  0 O 15.99
+10 0.870747 0.710969 0.723844  0 O 15.99
+11 0.870747 0.710969 0.276156  0 O 15.99
+12 0.129253 0.289031 0.723844  0 O 15.99
+13 0.629253 0.210969 0.223844  0 O 15.99
+14 0.370747 0.789031 0.776156  0 O 15.99
+15 0.370747 0.789031 0.223844  0 O 15.99
+16 0.629253 0.210969 0.776156  0 O 15.99
+17 0.000000 0.000000 0.226583  0 O 15.99
+18 0.000000 0.000000 0.773417  0 O 15.99
+19 0.500000 0.500000 0.273417  0 O 15.99
+20 0.500000 0.500000 0.726583  0 O 15.99
+21 0.016708 0.796760 0.000000  0 O 15.99
+22 0.983292 0.203240 0.000000  0 O 15.99
+23 0.516708 0.703240 0.500000  0 O 15.99
+24 0.483292 0.296760 0.500000  0 O 15.99

Test/diethyether.pdb

+COMPND    UNNAMED
+AUTHOR    GENERATED BY OPEN BABEL 2.3.90
+HETATM    1  C   UNL     1       1.710  -1.002  -0.016  1.00  0.00           C  
+HETATM    2  C   UNL     1       2.215   0.443   0.056  1.00  0.00           C  
+HETATM    3  O   UNL     1       2.632   1.700   0.119  1.00  0.00           O  
+HETATM    4  C   UNL     1       3.959   1.669   0.117  1.00  0.00           C  
+HETATM    5  C   UNL     1       5.491   1.658   0.117  1.00  0.00           C  
+HETATM    6  H   UNL     1       2.545  -1.671  -0.049  1.00  0.00           H  
+HETATM    7  H   UNL     1       1.116  -1.129  -0.897  1.00  0.00           H  
+HETATM    8  H   UNL     1       1.116  -1.216   0.848  1.00  0.00           H  
+HETATM    9  H   UNL     1       2.800   0.287  -0.826  1.00  0.00           H  
+HETATM   10  H   UNL     1       1.642   0.594   0.947  1.00  0.00           H  
+HETATM   11  H   UNL     1       3.949   1.096  -0.786  1.00  0.00           H  
+HETATM   12  H   UNL     1       3.968   2.231   1.028  1.00  0.00           H  
+HETATM   13  H   UNL     1       5.843   1.126  -0.742  1.00  0.00           H  
+HETATM   14  H   UNL     1       5.844   1.176   1.004  1.00  0.00           H  
+HETATM   15  H   UNL     1       5.855   2.664   0.087  1.00  0.00           H  
+CONECT    1    2    6    7    8                                       
+CONECT    2    1    3    9   10                                       
+CONECT    3    2    4                                                 
+CONECT    4    3    5   11   12                                       
+CONECT    5    4   13   14   15                                       
+CONECT    6    1                                                      
+CONECT    7    1                                                      
+CONECT    8    1                                                      
+CONECT    9    2                                                      
+CONECT   10    2                                                      
+CONECT   11    4                                                      
+CONECT   12    4                                                      
+CONECT   13    5                                                      
+CONECT   14    5                                                      
+CONECT   15    5                                                      
+MASTER        0    0    0    0    0    0    0    0   15    0   15    0
+END

Test/diethylether.cb

+#--------------------------------------------------------------------
+#
+#
+#SCRIPT FILE FOR POLYBUILD
+#
+#
+#--------------------------------------------------------------------
+# FILE PREFIX FOR OUTPUT FILES
+filename DE
+#--------------------------------------------------------------------
+# SIMULATION BOX DIMENSIONS (ANSGTROMS)
+simulation_box 100.0 100. 100
+#--------------------------------------------------------------------
+#  BLOCK DEFINITIONS
+# blocks : number of blocks
+#block definition : origin of block lx ly lz unitcell buffer
+# block origin block dimension unitcell file buffer size
+blocks    2
+  0   0   0 100 100  10 2.0 void.ucell 
+  0   0  90 100 100  10 2.0 void.ucell 
+#--------------------------------------------------------------------
+# DEFECT DEFINITIONS
+#--------------------------------------------------------------------
+# defects: number of defect groups
+# block index  defect symbol defect type number of  defects def threshold
+#defects 1 
+#1 S 1 20 10.5 
+#-----------------------------
+#  POLYMER DEFINITION
+#  ---------------------------------
+#  monomer file 
+opls yes
+monomer 1
+diethylether.mer R   
+#pe.mer
+# chain_type n_chains merperchain
+# amorph chain n_chain groups
+amorph_chain 1
+1 1000 1
+#1 40 1
+#2 10 1
+#amorph_chain 18 8
+# #  number of chains mpc radius
+#cont_chain  615  12 59.0

Test/diethylether.mer

+monomer 15 atoms diethylether
+vector1  0.000 0.000 0.000
+vector2  2.500 0.000 0.000
+     C    0.0        1.710  -1.002  -0.016  1            
+     C    0.0        2.215   0.443   0.056  1            
+     O    0.0        2.632   1.700   0.119  3            
+     C    0.0        3.959   1.669   0.117  1            
+     C    0.0        5.491   1.658   0.117  1            
+     H    0.0        2.545  -1.671  -0.049  2            
+     H    0.0        1.116  -1.129  -0.897  2            
+     H    0.0        1.116  -1.216   0.848  2            
+     H    0.0        2.800   0.287  -0.826  2            
+     H    0.0        1.642   0.594   0.947  2            
+     H    0.0        3.949   1.096  -0.786  2            
+     H    0.0        3.968   2.231   1.028  2            
+     H    0.0        5.843   1.126  -0.742  2            
+     H    0.0        5.844   1.176   1.004  2            
+     H    0.0        5.855   2.664   0.087  2           
+HEADH  1 0.0  -0.8994   0.6512  0.0067  2
+TAILH  2 0.0  2.1749   0.2380  0.0025  2
+mer_width 4.0
+merlength 4.625
+CONNECTIONS
+    1  4  2    6    7    8                                       
+    2  4  1    3    9   10                                       
+    3  2  2    4                                                 
+    4  4  3    5   11   12                                       
+    5  4  4   13   14   15                                       
+    6  1  1                                                      
+    7  1  1                                                      
+    8  1  1                                                      
+    9  1  2                                                      
+   10  1  2                                                      
+   11  1  4                                                      
+   12  1  4                                                      
+   13  1  5                                                      
+   14  1  5                                                      
+   15  1  5                                                      
+    H  1  1
+    T  1  8

Test/log.txt

-Simulation Box :     70.00   70.00  120.00
+Simulation Box :    100.82  105.51  100.00
 Monomer name : monomer         
-Number of atoms in monomer :  42
+Number of atoms in monomer :   6
  Base Vector - 1 :   0.0000  0.0000  0.0000
  Base Vector - 2 :   2.5000  0.0000  0.0000
 Head  -0.8994  0.6512  0.0067

Test/polyethylene.cb

+#--------------------------------------------------------------------
+#
+#
+#SCRIPT FILE FOR POLYBUILD
+#
+#
+#--------------------------------------------------------------------
+# FILE PREFIX FOR OUTPUT FILES
+filename PE
+#--------------------------------------------------------------------
+# SIMULATION BOX DIMENSIONS (ANSGTROMS)
+simulation_box 100.0 100. 100
+#--------------------------------------------------------------------
+#  BLOCK DEFINITIONS
+# blocks : number of blocks
+#block definition : origin of block lx ly lz unitcell buffer
+# block origin block dimension unitcell file buffer size
+blocks    2
+  0   0   0 100 100  10 2.0 void.ucell 
+  0   0  90 100 100  10 2.0 void.ucell 
+#--------------------------------------------------------------------
+# DEFECT DEFINITIONS
+#--------------------------------------------------------------------
+# defects: number of defect groups
+# block index  defect symbol defect type number of  defects def threshold
+#defects 1 
+#1 S 1 20 10.5 
+#-----------------------------
+#  POLYMER DEFINITION
+#  ---------------------------------
+#  monomer file 
+opls yes
+monomer 1
+pe.mer
+#diethylether.mer R   
+# chain_type n_chains merperchain
+# amorph chain n_chain groups
+amorph_chain 1
+1 100 100
+#1 40 1
+#2 10 1
+#amorph_chain 18 8
+# #  number of chains mpc radius
+#cont_chain  615  12 59.0

Test/polysio2.cb

+#--------------------------------------------------------------------
+#
+#
+#SCRIPT FILE FOR POLYBUILD
+#
+#
+#--------------------------------------------------------------------
+# FILE PREFIX FOR OUTPUT FILES
+filename SIO2PE
+#--------------------------------------------------------------------
+# SIMULATION BOX DIMENSIONS (ANSGTROMS)
+simulation_box 100.82  105.508 100
+#--------------------------------------------------------------------
+#  BLOCK DEFINITIONS
+# blocks : number of blocks
+#block definition : origin of block lx ly lz unitcell buffer
+# block origin block dimension unitcell file buffer size
+blocks    1
+  0   0   0 100.82 105.508 26.31 2.0 sio2.ucell 
+#  0   0  90 100 100  10 2.0 void.ucell 
+#--------------------------------------------------------------------
+# DEFECT DEFINITIONS
+#--------------------------------------------------------------------
+# defects: number of defect groups
+# block index  defect symbol defect type number of  defects def threshold
+#defects 1 
+#1 S 1 20 10.5 
+#-----------------------------
+#  POLYMER DEFINITION
+#  ---------------------------------
+#  monomer file 
+opls yes
+monomer 1
+pe.mer
+#diethylether.mer R   
+# chain_type n_chains merperchain
+# amorph chain n_chain groups
+amorph_chain 1
+1 100 100
+#1 40 1
+#2 10 1
+#amorph_chain 18 8
+# #  number of chains mpc radius
+#cont_chain  615  12 59.0

Test/sio2.ucell

+24  # number of Atoms
+1.0
+5.041400 0.000000 0.000000
+0.000000 8.792439 0.000000
+0.000000 0.000000 8.776380
+Direct 
+ 1 0.063427 0.824781 0.180519  0 Si 28.08
+ 2 0.936573 0.175219 0.819481  0 Si 28.08
+ 3 0.936573 0.175219 0.180519  0 Si 28.08
+ 4 0.063427 0.824781 0.819481  0 Si 28.08
+ 5 0.563427 0.675219 0.319481  0 Si 28.08
+ 6 0.436573 0.324781 0.680519  0 Si 28.08
+ 7 0.436573 0.324781 0.319481  0 Si 28.08
+ 8 0.563427 0.675219 0.680519  0 Si 28.08
+ 9 0.129253 0.289031 0.276156  0 O 15.99
+10 0.870747 0.710969 0.723844  0 O 15.99
+11 0.870747 0.710969 0.276156  0 O 15.99
+12 0.129253 0.289031 0.723844  0 O 15.99
+13 0.629253 0.210969 0.223844  0 O 15.99
+14 0.370747 0.789031 0.776156  0 O 15.99
+15 0.370747 0.789031 0.223844  0 O 15.99
+16 0.629253 0.210969 0.776156  0 O 15.99
+17 0.000000 0.000000 0.226583  0 O 15.99
+18 0.000000 0.000000 0.773417  0 O 15.99
+19 0.500000 0.500000 0.273417  0 O 15.99
+20 0.500000 0.500000 0.726583  0 O 15.99
+21 0.016708 0.796760 0.000000  0 O 15.99
+22 0.983292 0.203240 0.000000  0 O 15.99
+23 0.516708 0.703240 0.500000  0 O 15.99
+24 0.483292 0.296760 0.500000  0 O 15.99

Test/slab_polysio2.cb

+#--------------------------------------------------------------------
+#
+#
+#SCRIPT FILE FOR POLYBUILD
+#
+#
+#--------------------------------------------------------------------
+# FILE PREFIX FOR OUTPUT FILES
+filename SLAB_SIO2PE
+#--------------------------------------------------------------------
+# SIMULATION BOX DIMENSIONS (ANSGTROMS)
+simulation_box 100.82  105.508 100
+#--------------------------------------------------------------------
+#  BLOCK DEFINITIONS
+# blocks : number of blocks
+#block definition : origin of block lx ly lz unitcell buffer
+# block origin block dimension unitcell file buffer size
+blocks    4
+  0   0  10 100.82 105.508 26.31 2.0 sio2.ucell 
+  0   0  63 100.82 105.508 26.31 2.0 sio2.ucell 
+  0   0  90 100.82 105.508 8.0 2.0  void.ucell 
+  0   0   0 100.82 105.508 8.0 2.0  void.ucell 
+#--------------------------------------------------------------------
+# DEFECT DEFINITIONS
+#--------------------------------------------------------------------
+# defects: number of defect groups
+# block index  defect symbol defect type number of  defects def threshold
+#defects 1 
+#1 S 1 20 10.5 
+#-----------------------------
+#  POLYMER DEFINITION
+#  ---------------------------------
+#  monomer file 
+opls yes
+monomer 1
+pe.mer
+#diethylether.mer R   
+# chain_type n_chains merperchain
+# amorph chain n_chain groups
+amorph_chain 1
+1 100 40
+#1 40 1
+#2 10 1
+#amorph_chain 18 8
+# #  number of chains mpc radius
+#cont_chain  615  12 59.0