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378 | PROGRAM format_history
!***********************************************************************************
!
! module to format dl_meso HISTORY files
!
! authors - m. a. seaton & s. chiacchiera, february 2017
!
!**********************************************************************************
IMPLICIT none
INTEGER, PARAMETER :: dp = SELECTED_REAL_KIND (15, 307)
INTEGER, PARAMETER :: ntraj=10,nuser=5
CHARACTER(80) :: text, a2
CHARACTER(8), ALLOCATABLE :: namspe (:), nammol (:)
CHARACTER(6) :: chan
CHARACTER(8) :: a1
INTEGER, ALLOCATABLE :: ltp (:), ltm (:), mole (:), beads (:), bonds (:), bndtbl (:,:)
INTEGER, ALLOCATABLE :: nbdmol (:), nbomol (:)
INTEGER :: chain, imol, ioerror, i, k, j, nmoldef, ibond
INTEGER :: nspe, nbeads, nusyst, nsyst, nbonds, global, species, molecule, numnodes, numbond
INTEGER :: nummol, lfrzn, rnmol, keytrj, srfx, srfy, srfz
INTEGER :: bead1, bead2
INTEGER :: n1, n2, n3, n4
INTEGER :: nform
REAL(KIND=dp), ALLOCATABLE :: nmol (:)
REAL(KIND=dp) :: volm, dimx, dimy, dimz, shrdx, shrdy, shrdz
REAL(KIND=dp) :: amass, rcii
REAL(KIND=dp) :: time, mbeads, mglobal, x, y, z, vx, vy, vz, fx, fy, fz
REAL(KIND=dp) :: r1, r2, r3, r4
LOGICAL :: eof, lcomm, lmcheck
! Switches for commenting and checking molecules
lcomm = .TRUE.
lmcheck = .TRUE.
! Get number of nodes
WRITE (*,*) "Number of nodes used in calculations ?"
READ (*,*) numnodes
ALLOCATE (beads (numnodes), bonds (numnodes))
! Determine if HISTORY files exist
IF (numnodes>1) THEN
INQUIRE (file = 'HISTORY000000', EXIST = eof)
ELSE
INQUIRE (file = 'HISTORY', EXIST = eof)
END IF
IF (.NOT. eof) THEN
WRITE (*,*) "ERROR: cannot find HISTORY files"
STOP
END IF
! Open the output files
nform = ntraj + numnodes
DO j = 1, numnodes
WRITE (chan, '(i6.6)') j-1
IF (numnodes>1)THEN
OPEN (nform+j-1, file = 'HISTORY'//chan//"-F", status = 'replace')
ELSE
OPEN (nform+j-1, file = 'HISTORY'//"-F", status = 'replace')
END IF
END DO
! First reading, where the number of beads, molecules and bonds are determined
! Arrays are filled with names of particles and molecules
! If multiple HISTORY files are present, it is checked they are compatible
numbond = 0
DO j = 1, numnodes
WRITE (chan, '(i6.6)') j-1
IF (numnodes>1) THEN
OPEN (ntraj+j-1, file = 'HISTORY'//chan, access = 'sequential', form = 'unformatted', status = 'unknown')
ELSE
OPEN (ntraj, file = 'HISTORY', access = 'sequential', form = 'unformatted', status = 'unknown')
END IF
IF (j == 1) THEN
READ (ntraj+j-1) nspe, nmoldef, nusyst, nsyst, nbeads, nbonds
READ (ntraj+j-1) dimx, dimy, dimz, volm
READ (ntraj+j-1) keytrj, srfx, srfy, srfz
ELSE
READ (ntraj+j-1) n1, n2, n3, n4, nbeads, nbonds
READ (ntraj+j-1) r1, r2, r3, r4
IF (n1 /= nspe .OR. n2 /= nmoldef .OR. n3 /= nusyst .OR. n4 /= nsyst &
.OR. r1 /= dimx .OR. r2 /= dimy .OR. r3 /= dimz .OR. r4 /= volm) THEN
WRITE (*,*) "ERROR: HISTORY files do not refer to the same system!"
STOP
ENDIF
READ (ntraj+j-1) n1, n2, n3, n4
IF (n1 /= keytrj .OR. n2 /= srfx .OR. n3 /= srfy .OR. n4 /= srfz) THEN
WRITE (*,*) "ERROR: HISTORY files do not refer to the same system!"
STOP
ENDIF
ENDIF
beads (j) = nbeads
bonds (j) = nbonds
numbond = numbond + nbonds
IF (lcomm) WRITE (nform+j-1,*) "# nspe, nmoldef, nusyst, nsyst, nbeads, nbonds"
WRITE (nform+j-1,*) nspe, nmoldef, nusyst, nsyst, nbeads, nbonds
IF (lcomm) WRITE (nform+j-1,*) "# dimx, dimy, dimz, volm"
WRITE (nform+j-1,97) dimx, dimy, dimz, volm
IF (lcomm) WRITE (nform+j-1,*) "# keytrj, srfx, srfy, srfz"
WRITE (nform+j-1,*) keytrj, srfx, srfy, srfz
END DO ! loop over nodes
ALLOCATE (namspe (nspe), nammol (nmoldef))
IF (lmcheck) THEN
ALLOCATE (ltp (1:nsyst), ltm (1:nsyst), mole (1:nsyst))
ALLOCATE (nmol (1:nmoldef), nbdmol (1:nmoldef), nbomol (1:nmoldef))
ALLOCATE (bndtbl (numbond, 2))
ENDIF
DO j = 1, numnodes
IF (lcomm) WRITE (nform+j-1,*) "# SPECIES:"
IF (lcomm) WRITE (nform+j-1,*) "# namspe, amass, rcii, lfrzn"
DO i = 1, nspe
IF (j == 1) THEN
READ (ntraj+j-1) namspe (i), amass, rcii, lfrzn
ELSE
READ (ntraj+j-1) a1, amass, rcii, lfrzn
IF (a1 /= namspe (i))THEN
WRITE (*,*) "ERROR: HISTORY files do not refer to the same system!"
STOP
ENDIF
ENDIF
WRITE (nform+j-1,96) namspe (i), amass, rcii, lfrzn
END DO
IF (nmoldef>0) THEN
IF (lcomm) WRITE (nform+j-1,*) "# MOLECULES:"
IF (lcomm) WRITE (nform+j-1,*) "# nammol"
DO i = 1, nmoldef
IF (j==1) THEN
READ (ntraj+j-1) nammol (i)
ELSE
READ (ntraj+j-1) a1
IF (a1 /= nammol (i))THEN
WRITE (*,*) "ERROR: HISTORY files do not refer to the same system!"
STOP
ENDIF
END IF
WRITE (nform+j-1,*) nammol (i)
END DO
END IF
IF (j == 1) THEN
READ (ntraj+j-1) text
ELSE
READ (ntraj+j-1) a2
IF (a2 /= text) THEN
WRITE (*,*) "ERROR: HISTORY files do not refer to the same system!"
STOP
ENDIF
ENDIF
IF (lcomm) WRITE (nform+j-1,*) "# Simulation name:"
WRITE (nform+j-1,*) text
ENDDO ! end of loop over nodes
DO j = 1, numnodes
CLOSE (ntraj+j-1)
END DO
! Second reading, where (if required) arrays are filled with properties
! of beads and molecules. Then, the snapshots of trajectories are read.
DO j = 1, numnodes
WRITE (chan, '(i6.6)') j-1
IF (numnodes>1) THEN
OPEN (ntraj+j-1, file = 'HISTORY'//chan, access = 'sequential', form = 'unformatted', status = 'unknown')
ELSE
OPEN (ntraj, file = 'HISTORY', access = 'sequential', form = 'unformatted', status = 'unknown')
END IF
READ (ntraj+j-1) !nspe, nmoldef, nusyst, nsyst, nbeads, nbonds
READ (ntraj+j-1) !dimx, dimy, dimz, volm
READ (ntraj+j-1) !keytrj, srfx, srfy, srfz
DO i = 1, nspe
READ (ntraj+j-1) !namspe (i), amass, rcii, lfrzn
END DO
DO i = 1, nmoldef
READ (ntraj+j-1) !nammol (i)
END DO
READ (ntraj+j-1) !text
END DO
nummol = 0 !counter for number of molecules
ibond = 0 !counter for bonds
! fill in arrays for beads and bonds
DO j = 1, numnodes
IF (lcomm) WRITE (nform+j-1,*) "# BEADS:"
IF (lcomm) WRITE (nform+j-1,*) "# global, species, molecule, chain"
IF (lmcheck) THEN
!Build ltp, ltm, mole
DO i = 1, beads (j)
READ (ntraj+j-1) global, species, molecule, chain
ltp (global) = species
ltm (global) = molecule
mole (global) = chain
nummol = MAX (nummol, chain)
WRITE (nform+j-1,*) global, species, molecule, chain
END DO
ELSE
DO i = 1, beads (j)
READ (ntraj+j-1) global, species, molecule, chain
WRITE (nform+j-1,*) global, species, molecule, chain
END DO
ENDIF
IF (bonds (j)>0) THEN
IF (lcomm) WRITE (nform+j-1,*) "# BONDS:"
IF (lcomm) WRITE (nform+j-1,*) "# extremes of the bond"
IF (lmcheck) THEN
! Build bndtbl
DO i = 1, bonds (j)
ibond = ibond + 1
READ (ntraj+j-1) bead1, bead2
bndtbl (ibond, 1) = bead1
bndtbl (ibond, 2) = bead2
WRITE (nform+j-1,*) bead1, bead2
END DO
ELSE
DO i = 1, bonds (j)
READ (ntraj+j-1) bead1, bead2
WRITE (nform+j-1,*) bead1, bead2
END DO
END IF
END IF
END DO ! over nodes
IF (lmcheck) THEN
! determine numbers of molecules, beads and bonds per molecule type
nmol = 0.0_dp
nbdmol = 0
nbomol = 0
chain = 0
imol = 0 !necessary to avoid out of bounds
DO i = 1, nsyst
IF (mole (i) /= chain) THEN
chain = mole (i)
imol = ltm (i)
nmol (imol) = nmol (imol) + 1.0_dp
END IF
IF (imol > 0) nbdmol (imol) = nbdmol (imol) + 1
END DO
DO i = 1, numbond
imol = ltm (bndtbl (i,1))
nbomol (imol) = nbomol (imol) + 1
END DO
DO i = 1, nmoldef
rnmol = NINT (nmol (i))
IF (rnmol>0) THEN
nbdmol (i) = nbdmol (i) / rnmol
nbomol (i) = nbomol (i) / rnmol
END IF
END DO
! Write to std output the arrays built
WRITE (*,*) "# Check of beads: i, ltp(i), ltm(i), mole(i)"
DO i = 1, nsyst
WRITE(*,*) i, ltp (i), ltm (i), mole (i)
END DO
!Check of molecule beads and numbers
IF (nmoldef>0) THEN
WRITE (*,*) "# Check of molecules: nammol(i), nbdmol(i), nbomol(i), nmol(i)"
DO i = 1, nmoldef
WRITE (*,*) nammol (i), nbdmol (i), nbomol (i), NINT(nmol(i))
END DO
WRITE (*,*) "# Total number of molecules = ",nummol
END IF
! Write to std output bndtbl
IF (numbond > 0) THEN
WRITE (*,*) "# Check of bonds: bndbtl(i,1), bndbtl(i,2)"
DO i = 1, numbond
WRITE (*,*) bndtbl (i,1), bndtbl (i,2)
END DO
END IF
END IF
!reading trajectories
DO j = 1, numnodes
eof = .false.
k = 0
IF (lcomm) WRITE (nform+j-1,*) "# --- TRAJECTORIES --- (key =", keytrj,")"
SELECT CASE (keytrj)
CASE (0)
IF (lcomm) WRITE (nform+j-1,*) "# mglobal, x, y, z"
CASE(1)
IF (lcomm) WRITE (nform+j-1,*) "# mglobal, x, y, z, vx, vy, vz"
CASE(2)
IF (lcomm) WRITE (nform+j-1,*) "# mglobal, x, y, z, vx, vy, vz, fx, fy, fz"
END SELECT
DO WHILE (.true.)
READ (ntraj+j-1, IOSTAT=ioerror) time, mbeads, dimx, dimy, dimz, shrdx, shrdy, shrdz
IF (lcomm) WRITE (nform+j-1,*) "# time, mbeads, dimx, dimy, dimz, shrdx, shrdy, shrdz"
WRITE (nform+j-1,98) time, mbeads, dimx, dimy, dimz, shrdx, shrdy, shrdz
IF (ioerror/=0) THEN
eof = .true.
IF (k==0) THEN
PRINT *, 'ERROR: cannot find trajectory data in HISTORY files'
STOP
END IF
EXIT
END IF
k = k + 1
IF (lcomm) WRITE (nform+j-1,*) "# snapshot number:", k
nbeads = NINT (mbeads)
SELECT CASE (keytrj)
CASE (0)
DO i = 1, nbeads
READ (ntraj+j-1) mglobal, x, y, z
WRITE (nform+j-1,99) mglobal, x, y, z
END DO
CASE (1)
DO i = 1, nbeads
READ (ntraj+j-1) mglobal, x, y, z, vx, vy, vz
WRITE (nform+j-1,99) mglobal, x, y, z, vx, vy, vz
END DO
CASE (2)
DO i = 1, nbeads
READ (ntraj+j-1) mglobal, x, y, z, vx, vy, vz, fx, fy, fz
WRITE (nform+j-1,99) mglobal, x, y, z, vx, vy, vz, fx, fy, fz
END DO
END SELECT
END DO
END DO
! Close the trajectory files
DO j = 1, numnodes
CLOSE (ntraj+j-1)
END DO
! close the output files
DO j = 1, numnodes
CLOSE (nform+j-1)
END DO
DEALLOCATE (beads, bonds)
DEALLOCATE (namspe, nammol)
IF (lmcheck) DEALLOCATE (ltp, ltm, mole, nmol, nbdmol, bndtbl, nbomol)
99 FORMAT(f10.1,2x,1p,9(e13.6,3x))
98 FORMAT(8(f10.3,3x))
97 FORMAT(4(f10.3,3x))
96 FORMAT(A9,3x,2(f10.3,3x),I2)
END PROGRAM format_history
|
