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babel.f
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babel.f
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module Babel_m
use IFPORT
use type_m
use MM_input , only : MM_input_format
use parameters_m , only : file_type, &
ad_hoc , &
driver
use Allocation_m , only : Allocate_UnitCell
use tuning_m , only : ad_hoc_tuning
use Babel_routines_m , only : Symbol_2_AtNo , &
Identify_Fragments , &
AtNo_2_Symbol , &
MMSymbol_2_Symbol , &
Identify_Residues , &
Pack_residues , &
Sort_nr , &
TO_UPPER_CASE , &
Center_of_Gravity , &
Initialize_System
use Semi_Empirical_Parms , only : atom
! private
PUBLIC :: Read_from_XYZ , Read_from_Poscar , Read_from_PDB
PUBLIC :: Read_PDB , Read_XYZ
PUBLIC :: Coords_from_Universe
PUBLIC :: Resume_from_TRJ
type(universe) , allocatable , public :: trj(:)
real*8 , public :: MD_dt
integer , allocatable , public :: QMMM_key(:)
character(len=72) , public :: System_Characteristics
contains
!
!
!
!=====================================================
subroutine Coords_from_Universe( Unit_Cell , System )
!=====================================================
implicit none
type(structure) , intent(out) :: Unit_Cell
type(universe) , intent(inout) :: System
! local variables ...
integer :: j , n_residues
logical :: TorF
Unit_Cell%atoms = System%N_of_Atoms
select case( file_type )
case( "structure" )
n_residues = size( System%list_of_residues )
case( "trajectory" )
n_residues = size( trj(1)%list_of_residues )
end select
! allocating Unit_Cell structure ...
CALL Allocate_UnitCell( Unit_Cell , n_residues )
! coordinates and other info from input data ...
forall( j=1:unit_cell%atoms )
unit_cell % coord (j,:) = System % atom(j) % xyz(:)
unit_cell % AtNo (j) = System % atom(j) % AtNo
unit_cell % fragment (j) = System % atom(j) % fragment
unit_cell % Symbol (j) = System % atom(j) % Symbol
unit_cell % residue (j) = System % atom(j) % residue
unit_cell % nr (j) = System % atom(j) % nr
unit_cell % MMSymbol (j) = System % atom(j) % MMSymbol
unit_cell % solute (j) = System % atom(j) % solute
unit_cell % DPF (j) = System % atom(j) % DPF
unit_cell % El (j) = System % atom(j) % El
unit_cell % Hl (j) = System % atom(j) % Hl
unit_cell % flex (j) = System % atom(j) % flex
unit_cell % hardcore (j) = System % atom(j) % hardcore
unit_cell % solvation_hardcore (j) = System % atom(j) % solvation_hardcore
unit_cell % V_shift (j) = System % atom(j) % V_shift
unit_cell % QMMM (j) = System % atom(j) % QMMM
unit_cell % Nvalen (j) = atom(unit_cell%AtNo(j)) % Nvalen
unit_cell % polar (j) = atom(unit_cell%AtNo(j)) % polar
end forall
unit_cell%N_of_Solvent_Molecules = System%N_of_Solvent_Molecules
! get list of residues ...
select case( file_type )
case( "structure" )
If( size(unit_cell%list_of_fragments) /= size(system%list_of_fragments) ) then
deallocate(unit_cell%list_of_fragments)
allocate (unit_cell%list_of_fragments(size(system%list_of_fragments)))
end If
unit_cell%list_of_residues = System%list_of_residues
unit_cell%list_of_fragments = System%list_of_fragments
case( "trajectory" )
If( size(unit_cell%list_of_fragments) /= size(trj(1)%list_of_fragments) ) then
deallocate(unit_cell%list_of_fragments)
allocate (unit_cell%list_of_fragments(size(trj(1)%list_of_fragments)))
end If
unit_cell%list_of_residues = trj(1)%list_of_residues
unit_cell%list_of_fragments = trj(1)%list_of_fragments
end select
! sort the nr indices ...
if( MM_input_format == "GMX" ) CALL Sort_nr( unit_cell )
! nr indices must start with 1 ...
if( any(unit_cell % nr == 0) ) then
TorF = systemQQ("sed '11i >> halted: check input.pdb, nr indice = 0 found << ' .warning.signal |cat")
STOP
end if
! unit_cell dimensions ...
unit_cell % T_xyz = System % box
! standard Wolfgang-Helmholtz parameter ...
Unit_Cell % k_WH = 1.75d0
end subroutine Coords_from_Universe
!
!
!
!=====================================
subroutine Read_from_XYZ( Unit_Cell )
!=====================================
implicit none
type(structure) , intent(out) :: unit_cell
character(len=1) :: dumb_char
integer :: i , j
OPEN(unit=3,file='xyz.dat',status='old')
! start reading the structure characteristics
read(3,*) unit_cell%atoms ! <== No of atoms in the ORIGINAL supercell
read(3,'(A72)') System_Characteristics
! allocating arrays ...
CALL Allocate_UnitCell( Unit_Cell )
CALL Initialize_System( Unit_Cell )
! read unit_cell dimensions ...
read(3,*) ( unit_cell%T_xyz(i) , i=1,3 )
! testing for AtNo or Symbol ...
read(3,*) dumb_char
backspace 3
! reading coordinates ...
select case ( ichar(dumb_char) )
! Atomic Numbers ...
case( 48:57 )
DO j = 1 , unit_cell%atoms
read(3,*) unit_cell%AtNo(j), (unit_cell%coord(j,i), i=1,3)
END DO
CALL AtNo_2_Symbol(Unit_Cell)
! Chemical Symbols ...
case( 65:122 )
DO j = 1 , unit_cell%atoms
read(3,*) unit_cell%Symbol(j), (unit_cell%coord(j,i), i=1,3)
END DO
CALL Symbol_2_AtNo(Unit_Cell)
end select
CLOSE(3)
Unit_cell % Nvalen (:) = atom(unit_cell%AtNo(:)) % Nvalen
Unit_cell % polar (:) = atom(unit_cell%AtNo(:)) % polar
Unit_cell % MMSymbol = Unit_Cell % Symbol
include 'formats.h'
end subroutine Read_from_XYZ
!
!
!
!=====================================
subroutine Read_from_PDB( Unit_Cell )
!=====================================
implicit none
type(structure) , intent(out) :: Unit_Cell
! local variables ...
integer :: i , j , N_of_atoms
integer :: k = 0
integer :: file_err , io_err
character(len=5) :: MMSymbol_char
character(len=6) :: keyword
type(universe) :: system
logical :: TorF
OPEN(unit=3 , file='input.pdb',status='old' , iostat=file_err , err=11)
!-------------------------------------------------------------------------------------------
read(unit=3 , fmt = 43 , iostat=io_err , err=12) System_Characteristics
! reading unit cell vectors ...
read(unit=3 , fmt=105 , iostat=io_err , err=12) keyword
if ( keyword == "CRYST1" ) then
backspace 3
read(3 , fmt=100 , iostat=io_err , err=12) system%box(1) , system%box(2) , system%box(3)
end if
! scan file for N_of_Atoms ...
N_of_atoms = 0
do
read(unit=3 , fmt=105 , iostat=io_err , err=12) keyword
if ( keyword == "MASTER" ) exit
N_of_atoms = N_of_atoms + 1
if ( N_of_atoms > 20000 ) then
TorF = systemQQ("sed '11i *** reading of input.pdb halted forcibly ; ckeck input.pdb file format *** ' .warning.signal |cat")
STOP
end if
end do
system%N_of_atoms = N_of_atoms
allocate( system%atom(system%N_of_atoms) )
CALL Initialize_System( system )
!read data ...
rewind 3
do
read(unit=3 , fmt=105 , iostat=io_err , err=12) keyword
if( keyword == "CRYST1" ) then
do i = 1 , system%N_of_atoms
system%atom(i)%my_id = i
read(3 , 115 , iostat=io_err , err=12) &
MMSymbol_char , & ! <== atom type
system%atom(i)%residue , & ! <== residue name
system%atom(i)%nr , & ! <== residue sequence number
(system%atom(i)%xyz(j) , j=1,3) , & ! <== xyz coordinates
system%atom(i)%Symbol ! <== chemical element symbol
system%atom(i)%MMSymbol = adjustl(MMSymbol_char)
end do
end if
k = k + 1
if ( keyword == "MASTER" ) exit
if ( k > 20000 ) stop " *** reading of input.pdb halted ; ckeck file format *** "
end do
!-------------------------------------------------------------------------------------------
close(3)
! convert residues to upper case ...
forall( i=1:system%N_of_atoms ) system%atom(i)%residue = TO_UPPER_CASE( system%atom(i)%residue )
! use ad hoc tuning of EHT parameters ...
If( ad_hoc .and. (driver /= "MM_Dynamics") ) CALL ad_hoc_tuning( system )
! for use if atomic Symbols are not included in input.pdb ...
!If( sum( len_trim(system%atom%Symbol) ) == 0 ) CALL MMSymbol_2_Symbol( system%atom )
CALL MMSymbol_2_Symbol( system%atom )
! preprocessing the universe system ...
CALL Symbol_2_AtNo ( system%atom )
CALL Identify_Residues ( system )
CALL Identify_Fragments ( system )
!CALL Pack_Residues ( system%atom , system%list_of_residues )
! vector QMMM_key is the key to exchange QM and MM atomic properties ...
allocate( QMMM_key(system%N_of_atoms) , source=system%atom%my_id)
If( (verify(driver,'slice') == 6) .AND. (file_type == "trajectory") ) then
! replicate system throughout trj ...
CALL input_2_frames( system , trj )
else
! transfer Unit_Cell(structure) <-- system(universe)
CALL Coords_from_Universe( Unit_Cell , system )
end if
deallocate( system%atom , system%list_of_fragments , system%list_of_residues )
11 if( file_err > 0 ) stop "input.pdb file not found; terminating execution"
12 if( io_err > 0 ) stop "problems reading input.pdb; check IO_file_formats"
43 format(a72)
100 format(t7,3f9.3)
105 format(a6)
115 FORMAT(t12,a5,t18,a3,t23,i7,t31,f8.3,t39,f8.3,t47,f8.3,t77,a2)
end subroutine Read_from_PDB
!
!
!
!========================================
subroutine Read_from_Poscar( Unit_Cell )
!========================================
implicit none
type(structure) , intent(out) :: unit_cell
! local variables ...
real*8 :: x0 , y0 , z0
real*8 :: a , b , c
real*8 :: k_WH
integer :: n_kWH , n_residues , i , j , j1 , j2 , n , boundary_atom , openstatus
integer :: N_of_atoms , N_of_elements , N_of_cluster_atoms , N_of_Configurations
character(len=1) :: TorF , fragment
character(len=3) :: residue
logical :: flag , TF_flag
real*8 , allocatable :: xyz(:,:)
integer , allocatable :: atom_No(:)
character(len=2) , allocatable :: element(:) , symbol(:)
open(unit = 3, file = 'poscar.in', status = 'old', action = 'read', iostat = openstatus)
if (openstatus > 0) then
TF_flag = systemQQ("sed '11i *** Cannot open the file poscar.in *** ' .warning.signal |cat")
STOP
end if
! start reading the structure characteristics
read(3,*) System_Characteristics
read(3,*) N_of_Configurations ! <== No of configurations
read(3,*) unit_cell%atoms ! <== No of atoms in the ORIGINAL supercell
read(3,*) n_residues
! allocating arrays ...
CALL Allocate_UnitCell( Unit_Cell , n_residues )
! residues must be packed together ...
do i = 1 , n_residues
read(3,*) j1 , j2 , residue , fragment
unit_cell % list_of_residues (i) = residue
unit_cell % list_of_fragments (i) = residue
forall(j=j1:j2) unit_cell % residue (j) = residue
forall(j=j1:j2) unit_cell % fragment (j) = fragment
end do
! defining the k_WH parameter for the atom
! No of k_WH to be used
read(3,*) n_kWH
do i = 1 , n_kWH
read(3,*) j1 , j2 , k_WH
forall(j=j1:j2) unit_cell%k_WH(j) = k_WH
end do
! reads the unit cell vectors
read(3,*) x0 , y0 , z0
a = dsqrt(x0*x0 + y0*y0 + z0*z0)
read(3,*) x0 , y0 , z0
b = dsqrt(x0*x0 + y0*y0 + z0*z0)
read(3,*) x0 , y0 , z0
c = dsqrt(x0*x0 + y0*y0 + z0*z0)
! reads the chemical elements
read(3,*) N_of_elements
allocate(element(N_of_elements),atom_No(N_of_elements))
read(3,*) (element(i),i=1,N_of_elements)
! reads the number of atoms for each species
read(3,*) (atom_No(i),i=1,N_of_elements)
N_of_atoms = sum(atom_No(1:N_of_elements))
if( N_of_atoms /= unit_cell%atoms) pause 'Number of atoms do not match !!!'
allocate(xyz(N_of_atoms,3),symbol(N_of_atoms))
! reads the atom that sets the interface
read(3,*) boundary_atom
! reads the coordinates from vasp-POSCAR
do i = 1 , N_of_atoms
read(3,*) xyz(i,1) , xyz(i,2) , xyz(i,3) , TorF , TorF , TorF
do j = 1 , N_of_elements
if( (sum(atom_No(:j-1))+1 <= i) .AND. (i <= sum(atom_No(:j))) ) symbol(i) = element(j)
end do
end do
close(3)
! rescale coordinates by the unit cell vectors
xyz(:,1) = xyz(:,1)*a
xyz(:,2) = xyz(:,2)*b
xyz(:,3) = xyz(:,3)*c
! separate cluster from molecule atoms
n = 1
do i = 1 , N_of_atoms
flag = xyz(i,3) > xyz(boundary_atom,3) ! <== cluster atoms first
if (flag) then
unit_cell%symbol(n) = symbol(i)
unit_cell%coord(n,:) = xyz(i,:)
n = n + 1
end if
end do
N_of_cluster_atoms = n - 1
do i = 1 , N_of_atoms
flag = xyz(i,3) <= xyz(boundary_atom,3) ! <== molecule atoms at the end
if (flag) then
unit_cell%symbol(n) = symbol(i)
unit_cell%coord(n,:) = xyz(i,:)
n = n + 1
end if
end do
deallocate(xyz,symbol,element,atom_No)
include 'formats.h'
end subroutine Read_from_Poscar
!
!
!
!========================
subroutine Read_PDB(trj)
!========================
implicit none
type(universe) , allocatable , intent(out) :: trj(:)
! local variables ...
integer :: i , j , k , dumb_number , openstatus , inputstatus , model , number_of_atoms
real*8 :: time_1 , time_2 , delta_t
character(1) :: test
character(4) :: keyword
character(5) :: MMSymbol_char
logical :: TorF
open(unit = 31, file = 'frames.pdb', status = 'old', action = 'read', iostat = openstatus)
if (openstatus > 0) then
TorF = systemQQ("sed '11i *** Cannot open the file frames.pdb *** ' .warning.signal |cat")
STOP
end if
read(unit = 31, fmt = 43, iostat = inputstatus) System_Characteristics
! find the number of model frames ...
model = 0
do
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
if ( inputstatus /= 0 ) exit
if ( keyword == 'MODE' ) model = model + 1
end do
! return to the top of the file ...
rewind 31
! read number the atoms and time ...
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
do
if ( keyword == 'MODE' ) then
exit
else
! reading the time ...
if ( keyword == 'TITL' ) then
backspace 31
do
read(unit = 31, fmt = 42,advance='no',iostat = inputstatus) test
if(test == "=") then
read(unit = 31, fmt = 41, iostat = inputstatus) time_1
exit ! <== time_1 read
end if
end do
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
else
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
end if
end if
end do
number_of_atoms = 0
do
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
if ( keyword == 'ATOM' ) then
backspace 31
read(unit = 31, fmt = 32, iostat = inputstatus) dumb_number
number_of_atoms = number_of_atoms + 1
else
! reading the time ...
if ( keyword == 'TITL' ) then
backspace 31
do
read(unit = 31, fmt = 42,advance='no',iostat = inputstatus) test
if(test == "=") then
read(unit = 31, fmt = 41, iostat = inputstatus) time_2
exit ! <== time_2 read
end if
end do
exit ! <== leave outer do loop
end if
end if
end do
delta_t = time_2 - time_1
! Molecular Dynamics time step (pico-sec) ...
MD_dt = delta_t + epsilon(1.d0)
! return to the top of the file ...
rewind 31
! allocate array of frames ...
allocate( trj(model) )
trj(:)%System_Characteristics = System_Characteristics
do j = 1 , model
if( j == 1 ) then
do
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
if( keyword == 'CRYS' ) then
backspace 31
read(unit = 31, fmt = 40, iostat = inputstatus) ( trj(j)%box(i) , i=1,3 )
end if
if( keyword == 'MODE' ) exit
end do
allocate( trj(j)%atom(number_of_atoms) )
CALL Initialize_System( trj(j) )
do i = 1 , number_of_atoms
read(unit = 31, fmt = 33, iostat = inputstatus) MMSymbol_char , &
trj(j) % atom(i) % residue , &
trj(j) % atom(i) % nr , &
( trj(j) % atom(i) % xyz(k) , k=1,3 )
trj(j) % atom(i) % MMSymbol = adjustl(MMSymbol_char)
end do
! convert residues to upper case ...
forall( i=1:number_of_atoms ) trj(j)%atom(i)%residue = TO_UPPER_CASE( trj(j)%atom(i)%residue )
CALL MMSymbol_2_Symbol ( trj(j)%atom )
CALL Symbol_2_AtNo ( trj(j)%atom )
! use ad hoc tuning of EHT parameters ...
If( ad_hoc .and. (driver /= "MM_Dynamics") ) CALL ad_hoc_tuning( trj(j) )
trj(j)%atom % Nvalen = atom(trj(j)%atom%AtNo) % Nvalen
trj(j)%atom % polar = atom(trj(j)%atom%AtNo) % polar
else
do
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
if( keyword == 'CRYS' ) then
backspace 31
read(unit = 31, fmt = 40, iostat = inputstatus) ( trj(j)%box(i) , i=1,3 )
end if
if ( keyword == 'MODE' ) exit
end do
allocate( trj(j)%atom(number_of_atoms) )
CALL Initialize_System( trj(j) )
do i = 1 , number_of_atoms
read(unit = 31, fmt = 37, iostat = inputstatus) ( trj(j)%atom(i)%xyz(k) , k=1,3 )
end do
end if
end do
close(31)
trj%N_of_atoms = number_of_atoms
! convert residues to upper case ...
forall( i=1:trj(1)%N_of_atoms ) trj(1)%atom(i)%residue = TO_UPPER_CASE( trj(1)%atom(i)%residue )
! get list of residues in trj ...
CALL Identify_Residues( trj(1) )
! get list of fragments in trj ...
CALL Identify_Fragments( trj(1) )
! Copy information from trj(1) to trj(:) ...
forall(i = 2:model )
trj(i) % atom % AtNo = trj(1) % atom % AtNo
trj(i) % atom % MMSymbol = trj(1) % atom % MMSymbol
trj(i) % atom % residue = trj(1) % atom % residue
trj(i) % atom % nr = trj(1) % atom % nr
trj(i) % atom % Symbol = trj(1) % atom % Symbol
trj(i) % atom % fragment = trj(1) % atom % fragment
trj(i) % atom % solute = trj(1) % atom % solute
trj(i) % atom % DPF = trj(1) % atom % DPF
trj(i) % atom % El = trj(1) % atom % El
trj(i) % atom % Hl = trj(1) % atom % Hl
trj(i) % atom % hardcore = trj(1) % atom % hardcore
trj(i) % atom % solvation_hardcore = trj(1) % atom % solvation_hardcore
trj(i) % atom % V_shift = trj(1) % atom % V_shift
trj(i) % atom % QMMM = trj(1) % atom % QMMM
trj(i) % atom % Nvalen = atom(trj(1)%atom%AtNo) % Nvalen
trj(i) % atom % polar = atom(trj(1)%atom%AtNo) % polar
end forall
! GROUP residues ...
do i = 1 , size(trj)
CALL Pack_Residues( trj(i)%atom , trj(1)%list_of_residues )
end do
! Information about the Solvent System ...
! solvent molecules must be contiguous ...
trj%N_of_Solvent_Molecules = maxval( trj(1) % atom % nr, trj(1) % atom % fragment == 'S' ) &
- minval( trj(1) % atom % nr, trj(1) % atom % fragment == 'S' ) + 1
do i = 1 , size(trj)
allocate( trj(i) % solvent( trj(i)%N_of_Solvent_Molecules ) )
trj(i)%solvent%N_of_Atoms = count( trj(i)%atom%fragment == 'S' ) / trj(i)%N_of_Solvent_molecules
CALL Center_of_Gravity( trj(i) )
end do
! Formats ...
32 format(5x, i6)
33 format(t12,a5,t18,a3,t23,i7,t31,f8.3,t39,f8.3,t47,f8.3)
35 format(a4)
36 format(7x, i7)
37 format(t31,f8.3,t39,f8.3,t47,f8.3)
38 format(10x, a1)
39 format(81x, f7.0)
40 format(6x, 3f9.3)
41 format(f13.7)
42 format(a1)
43 format(a72)
end subroutine Read_PDB
!
!
!
!========================
subroutine Read_XYZ(trj)
!========================
implicit none
type(universe) , allocatable , intent(out) :: trj(:)
! local variables ....
character(1) :: idx
integer :: openstatus , inputstatus , atoms , i , j , k , model
integer :: j1 , j2 , n_residues
character(1) :: fragment
character(3) :: residue
logical :: TorF
open(unit = 13, file = 'XYZ.trj', status = 'old', action = 'read', iostat = openstatus)
if( openstatus > 0 ) then
TorF = systemQQ("sed '11i *** Cannot open the file XYZ.trj *** ' .warning.signal |cat")
STOP
end if
! read the number of models ...
model = 0
do
read(unit = 13, fmt = 21, iostat = inputstatus) idx
if( inputstatus /= 0 ) exit
if( idx == '$' ) then
model = model + 1
end if
end do
model = model - 1
! read the number the atoms ...
rewind 13
do
read(unit = 13, fmt = 21, iostat = inputstatus) idx
if( idx == '$' ) exit
end do
atoms = 0
do
read(unit = 13, fmt = 21, iostat = inputstatus) idx
if( idx /= '$' ) then
atoms = atoms + 1
else
exit
end if
end do
! prepare to read the system ...
allocate( trj(model) )
allocate( trj(1)%atom(atoms) )
CALL Initialize_System( trj(1) )
! start reading the structure characteristics ...
rewind 13
read(13,*) System_Characteristics
trj(1) % System_Characteristics = System_Characteristics
! residues must be packed together ...
read(13,*) n_residues
do i = 1 , n_residues
read(13,*) j1 , j2 , residue , fragment
forall(j=j1:j2) trj(1) % atom(j) % residue = residue
forall(j=j1:j2) trj(1) % atom(j) % fragment = fragment
end do
! read PBC vectors ...
read(13,*) trj(1)%box(1) , trj(1)%box(2) , trj(1)%box(3)
! read coordinate from the frames ...
do j = 1 , model
if( j == 1 ) then
read(unit = 13, fmt = 21, iostat = inputstatus) idx
do i = 1 , atoms
read(unit = 13, fmt = 22, iostat = inputstatus) trj(j)%atom(i)%Atno, ( trj(j)%atom(i)%xyz(k) , k=1,3 )
end do
CALL AtNo_2_Symbol(trj(j)%atom)
else
read(unit = 13, fmt = 21, iostat = inputstatus) idx
allocate( trj(j)%atom(atoms) )
CALL Initialize_System( trj(j) )
do i = 1 , atoms
read(unit = 13, fmt = 23, iostat = inputstatus) ( trj(j)%atom(i)%xyz(k) , k=1,3 )
end do
end if
! use ad hoc tuning of EHT parameters ...
If( ad_hoc .and. (driver /= "MM_Dynamics") ) CALL ad_hoc_tuning( trj(j) )
end do
trj(1)%N_of_atoms = atoms
! convert residues to upper case ...
forall( i=1:trj(1)%N_of_atoms ) trj(1)%atom(i)%residue = TO_UPPER_CASE( trj(1)%atom(i)%residue )
! get list of residues in trj ...
CALL Identify_Residues( trj(1) )
! get list of fragments in trj ...
CALL Identify_Fragments( trj(1) )
! Copy information from trj(1) to trj(:) ...
forall(i = 2:model )
trj(i) % N_of_atoms = trj(1) % N_of_atoms
trj(i) % box = trj(1) % box
trj(i) % atom % Atno = trj(1) % atom % Atno
trj(i) % atom % Symbol = trj(1) % atom % Symbol
trj(i) % atom % fragment = trj(1) % atom % fragment
trj(i) % atom % residue = trj(1) % atom % residue
trj(i) % atom % hardcore = trj(1) % atom % hardcore
trj(i) % atom % V_shift = trj(1) % atom % V_shift
trj(i) % atom % QMMM = trj(1) % atom % QMMM
end forall
! GROUP residues ...
do i = 1 , size(trj)
CALL Pack_Residues( trj(i)%atom , trj(1)%list_of_residues )
end do
! formats ...
21 format(a1)
22 format(i2, t4, f8.5, t13, f8.5, t22, f8.5)
23 format(3x, f8.5, t13, f8.5, t22, f8.5)
end subroutine Read_XYZ
!
!
!
!========================================
subroutine Resume_from_TRJ ( Unit_Cell )
!========================================
implicit none
type(structure) , intent(out) :: Unit_Cell
! local variables ...
integer :: i , j , k , openstatus , inputstatus , model , number_of_atoms
real*8 :: dumb_xyz(3) , dumb_box(3)
character(4) :: keyword
character(5) :: MMSymbol_char
type(universe) :: system
logical :: TorF
open(unit = 31, file = 'frames.pdb', status = 'old', action = 'read', iostat = openstatus)
if (openstatus > 0) then
TorF = systemQQ("sed '11i *** Cannot open the file frames.pdb *** ' .warning.signal |cat")
STOP
end if
read(unit = 31, fmt = 43, iostat = inputstatus) system% System_Characteristics
!----------------------------------------------------------------------------
! find the number of model frames ...
model = 0
do
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
if ( inputstatus /= 0 ) exit
if ( keyword == 'MODE' ) model = model + 1
end do
! return to the top of the file ...
rewind 31
!----------------------------------------------------------------------------
! read number of atoms and time ...
do
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
if ( keyword == 'MODE' ) exit
end do
number_of_atoms = 0
do
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
if ( keyword == 'ATOM' ) then
number_of_atoms = number_of_atoms + 1
else
exit
end if
end do
allocate( system% atom(number_of_atoms) )
CALL Initialize_System( system )
system% N_of_atoms = number_of_atoms
!----------------------------------------------------------------------------
! return to the top of the file ...
rewind 31
do j = 1 , model
if( j < model ) then
do
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
if( keyword == 'CRYS' ) then
backspace 31
read(unit = 31, fmt = 40, iostat = inputstatus) ( dumb_box(i) , i=1,3 )
end if
if( keyword == 'MODE' ) exit
end do
do i = 1 , number_of_atoms
read(unit = 31, fmt = 37, iostat = inputstatus) ( dumb_xyz(k) , k=1,3 )
end do
elseif( j == model ) then ! <== last frame ...
do
read(unit = 31, fmt = 35, iostat = inputstatus) keyword
if( keyword == 'CRYS' ) then
backspace 31
read(unit = 31, fmt = 40, iostat = inputstatus) ( system% box(i) , i=1,3 )
end if
if ( keyword == 'MODE' ) exit
end do
do i = 1 , number_of_atoms
system% atom(i)% my_id = i
read(unit = 31, fmt = 33, iostat = inputstatus) MMSymbol_char , &
system % atom(i) % residue , &
system % atom(i) % nr , &
( system % atom(i) % xyz(k) , k=1,3 )
system % atom(i) % MMSymbol = adjustl(MMSymbol_char)
end do
! convert residues to upper case ...
forall( i=1:number_of_atoms ) system %atom(i)% residue = TO_UPPER_CASE( system% atom(i)% residue )
CALL MMSymbol_2_Symbol ( system% atom )
CALL Symbol_2_AtNo ( system% atom )
! use ad hoc tuning of EHT parameters ...
If( ad_hoc .and. (driver /= "MM_Dynamics") ) CALL ad_hoc_tuning( system )
system%atom % Nvalen = atom(system%atom%AtNo) % Nvalen
system%atom % polar = atom(system%atom%AtNo) % polar
end if
end do
close(31)
! preprocessing the universe system ...
CALL Symbol_2_AtNo ( system%atom )
CALL Identify_Residues ( system )
CALL Identify_Fragments ( system )
! GROUP residues ...
!CALL Pack_Residues( system%atom , system%list_of_residues )
! vector QMMM_key is the key to exchange QM and MM atomic properties ...
allocate( QMMM_key(system%N_of_atoms) , source=system%atom%my_id)
CALL Coords_from_Universe( Unit_Cell , system )
! save copy of the just-generated initial configuration ...
CALL Dump_pdb( system )
! Formats ...
33 format(t12,a5,t18,a3,t23,i7,t31,f8.3,t39,f8.3,t47,f8.3)
35 format(a4)
37 format(t31,f8.3,t39,f8.3,t47,f8.3)
40 format(6x, 3f9.3)
43 format(a72)
end subroutine Resume_from_TRJ
!
!
!
!
!=========================================
subroutine input_2_frames( system , trj )
!=========================================
use parameters_m , only: t_i , t_f , n_t
implicit none
type(universe) , intent(in) :: system
type(universe) , allocatable , intent(out) :: trj(:)
! local variables ...
integer :: i
real*8 :: delta_t
delta_t = ( t_f - t_i ) / float(n_t)
! Molecular Dynamics time step (pico-sec) ...
MD_dt = delta_t
! allocate array of frames ...
allocate( trj(n_t) )
do i = 1 , n_t
allocate( trj(i)%atom(system%N_of_atoms) )
CALL Initialize_System( trj(i) )
end do
! Copy information from input.pdb to trj(:) ...
forall( i = 1:n_t ) trj(i) = system
end subroutine input_2_frames
!
!
!
!=======================
subroutine Dump_pdb(sys)
!=======================
implicit none
type(universe) , intent(inout) :: sys
! local variables ...
integer :: i , k
OPEN(unit=4,file='input.pdb',status='unknown')
write(4,6) "Generated by Resume_from_TRJ, ",sys%System_Characteristics
write(4,1) 'CRYST1' , sys%box(1) , sys%box(2) , sys%box(3) , 90.0 , 90.0 , 90.0 , 'P 1' , '1'
do i = 1 , sys%N_of_atoms
write(4,2) 'HETATM' , & ! <== non-standard atom
i , & ! <== global number
sys%atom(i)%MMSymbol , & ! <== atom type
' ' , & ! <== alternate location indicator
sys%atom(i)%residue , & ! <== residue name
' ' , & ! <== chain identifier
sys%atom(i)%nr , & ! <== residue sequence number
' ' , & ! <== code for insertion of residues
( sys%atom(i)%xyz(k) , k=1,3 ) , & ! <== xyz coordinates
1.00 , & ! <== occupancy
0.00 , & ! <== temperature factor
' ' , & ! <== segment identifier
' ' , & ! <== here only for tabulation purposes
sys%atom(i)%Symbol , & ! <== chemical element symbol
' ' ! <== charge on the atom
end do
write(4,3) 'MASTER', 0 , 0 , 0 , 0 , 0 , 0 , 0 , 0 , sys%N_of_atoms , 0 , sys%N_of_atoms , 0
write(4,*) 'END'
close(4)
1 FORMAT(a6,3F9.3,3F7.2,a11,a4)
2 FORMAT(a6,i5,a5,a1,a3,a2,i4,a4,3F8.3,2F6.2,a4,a6,a2,a2)
3 FORMAT(a6,i9,11i5)
6 FORMAT(a32,a72)
end subroutine Dump_pdb
!
!