Commit 525bdc38 authored by Dundar Yilmaz's avatar Dundar Yilmaz

bug fix with masses

parent 2574f633
File added
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......@@ -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
......
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......@@ -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
......
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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
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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
#--------------------------------------------------------------------
#
#
#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
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
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
......
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#--------------------------------------------------------------------
#
#
#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
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#--------------------------------------------------------------------
#
#
#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
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
#--------------------------------------------------------------------
#
#
#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
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