Formatting the HISTORY files of DL_MESO_DPD¶
Purpose of Module¶
This module format_history.f90
is a post-processing
utility for DL_MESO_DPD, the Dissipative Particle Dynamics (DPD) code from the DL_MESO package.
It converts the trajectory (HISTORY) file from unformatted to a human readable form, (optionally) including explanatory comments about all the quantities. This module is mainly for learning/checking purposes. The first aim is to help the user to check that the system was prepared as intended (e.g., showing all the bead properties and initial positions, all the bonds etc.). The idea is to use it on small systems when familiarizing with the structure of input files needed for the simulation. Secondly, it can be used as a starting point for user-defined analyses of trajectories.
Background Information¶
The base code for this module is DL_MESO_DPD, the Dissipative Particle Dynamics code from the mesoscopic simulation package DL_MESO, developed by M. Seaton at Daresbury Laboratory. This open source code is available from STFC under both academic (free) and commercial (paid) licenses. The module is to be used with DL_MESO in its currently released version, version 2.7 (dating December 2018).
A version of the module that works with HISTORY files generated by the
previous version of DL_MESO, version 2.6 (dating November 2015), can be
found in the old-v2.6
directory.
Testing¶
The present module is compiled with the available Fortran 2003 compiler, e.g.:
gfortran -o format.exe format_history.f90
and the executable must be in the same directory of the HISTORY file to be analyzed. To test the module, run the simulation with the toy input files given in the following. (Note that these files contain commented lines as suggestions for further tests.) For the CONTROL file
Simple test
volume 3.0 3.0 3.0
temperature 1.0
cutoff 1.0
timestep 0.01
steps 6
equilibration steps 2
traj 2 2 0
stats every 2
stack size 2
print every 2
job time 100.0
close time 10.0
#surface shear y
#surface frozen x
#surface hard x
ensemble nvt mdvv
finish
and for the FIELD file
Simple test
SPECIES 3
A 1.0 0.0 1 0
B 1.0 0.0 0 0
C 1.0 0.0 0 0
MOLECULES 2
AB
nummols 1
beads 2
A 0.0 0.0 0.0
B 0.1 0.0 0.0
bonds 1
harm 1 2 5.0 0.0
finish
AC
nummols 1
beads 2
A 0.0 0.0 0.0
C 0.1 0.0 0.0
bonds 1
harm 1 2 3.0 0.0
finish
INTERACTIONS 3
A A dpd 25.0 1.0 4.5
B B dpd 25.0 1.0 4.5
C C dpd 25.0 1.0 4.5
#EXTERNAL
#shear 3.0 0.0 0.0
CLOSE
After analyzing the trajectories, for a serial run (i.e., on a single
processor core) and for lcomm
, lmcheck
and sorted
all set
to .TRUE.
, this output should be printed on the screen
# Check of beads: i, ltp(i), ltm(i), mole(i)
1 1 0 0
2 1 1 1
3 2 1 1
4 1 2 2
5 3 2 2
# Check of molecules: nammol(i), nbdmol(i), nbomol(i), nmol(i)
AB 2 1 1
AC 2 1 1
# Total number of molecules = 2
# Check of bonds: bndbtl(i,1), bndbtl(i,2)
2 3
4 5
and the HISTORY-F file should be
# Simulation name:
Simple test
# nspe, nmoldef, nusyst, nsyst, numbond
3 2 1 5 2
# keytrj, srfx, srfy, srfz
0 0 0 0
# SPECIES:
# namspe, amass, rcii, chge, lfrzn
A 1.000 1.000 0.000 0
B 1.000 1.000 0.000 0
C 1.000 1.000 0.000 0
# MOLECULES:
# nammol
AB
AC
# BEADS:
# global, species, molecule, chain
1 1 0 0
2 1 1 1
3 2 1 1
4 1 2 2
5 3 2 2
# BONDS:
# extremes of the bond
2 3
4 5
# --- TRAJECTORIES --- (key = 0 )
# mglobal, x, y, z
# time, nbeads, dimx, dimy, dimz, shrdx, shrdy, shrdz
0.000 5 3.000 3.000 3.000 0.000 0.000 0.000
# snapshot number: 1
1 -5.594619E-03 -1.752832E-03 6.889737E-03
2 -1.691781E-01 6.786290E-01 1.166801E-02
3 -2.345695E-01 7.399172E-01 -1.447126E-01
4 5.198776E-01 -8.222446E-01 1.038467E-02
5 4.631501E-01 -8.058678E-01 1.464801E-01
# time, nbeads, dimx, dimy, dimz, shrdx, shrdy, shrdz
0.020 5 3.000 3.000 3.000 0.000 0.000 0.000
# snapshot number: 2
1 -1.061544E-02 -6.284880E-03 1.390368E-02
2 -1.395560E-01 6.796778E-01 4.361174E-02
3 -2.443224E-01 7.728033E-01 -1.800995E-01
4 5.280036E-01 -8.191712E-01 -3.253643E-02
5 4.401757E-01 -8.383441E-01 1.858304E-01
# time, nbeads, dimx, dimy, dimz, shrdx, shrdy, shrdz
0.040 5 3.000 3.000 3.000 0.000 0.000 0.000
# snapshot number: 3
1 -1.483900E-02 -1.635085E-02 2.109335E-02
2 -1.083779E-01 6.830112E-01 8.086194E-02
3 -2.571191E-01 8.101380E-01 -2.211317E-01
4 5.390852E-01 -8.157553E-01 -8.230434E-02
5 4.149363E-01 -8.723621E-01 2.321906E-01
If the simulation is run in parallel, the particles may not necessarily be written to the HISTORY file in order of particle index, but the module can sort the particles in each trajectory snapshot before printing to the HISTORY-F file.
Source Code¶
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!***********************************************************************************
!
! module to format dl_meso HISTORY files
!
! authors - m. a. seaton & s. chiacchiera, february 2017 (amended january 2021)
!
!**********************************************************************************
IMPLICIT none
INTEGER, PARAMETER :: dp = SELECTED_REAL_KIND (15, 307)
INTEGER, PARAMETER :: li = SELECTED_INT_KIND (12)
INTEGER, PARAMETER :: ntraj=10,nuser=5
INTEGER, PARAMETER :: endversion = 1
CHARACTER(80) :: text
CHARACTER(8), ALLOCATABLE :: namspe (:), nammol (:)
INTEGER, ALLOCATABLE :: ltp (:), ltm (:), mole (:), bndtbl (:,:)
INTEGER, ALLOCATABLE :: nbdmol (:), nbomol (:), readint (:), globindex (:)
INTEGER :: chain, imol, ioerror, i, k, nmoldef, numframe
INTEGER :: nspe, nbeads, nusyst, nsyst, global, species, molecule, numbond
INTEGER :: nummol, lfrzn, rnmol, keytrj, srfx, srfy, srfz
INTEGER :: bead1, bead2
INTEGER :: nform
INTEGER :: endver, Dlen, nstep, framesize, lend, leni
INTEGER(KIND=li) :: filesize, mypos, headerpos, currentpos, lend_li, leni_li, framesizeli, numbeadsli
REAL(KIND=dp), ALLOCATABLE :: nmol (:), readdata (:)
REAL(KIND=dp) :: dimx, dimy, dimz, shrdx, shrdy, shrdz
REAL(KIND=dp) :: amass, rcii, chge
REAL(KIND=dp) :: time
LOGICAL :: eof, lcomm, lmcheck, swapend, bigend, sorted
! Switches for commenting, checking molecules and sorting particles in output
lcomm = .TRUE.
lmcheck = .TRUE.
sorted = .TRUE.
! determine number of bytes for selected double precision kind
! (the default SELECTED_REAL_KIND (15, 307) should return 8 bytes)
lend = STORAGE_SIZE (1.0_dp) / 8
leni = BIT_SIZE (1) / 8
lend_li = INT (lend, KIND=li)
leni_li = INT (leni, KIND=li)
! check endianness of machine
bigend = (IACHAR(TRANSFER(1,"a"))==0)
! Determine if HISTORY file exists, which endianness to use,
! if type of real is correct
INQUIRE (file = 'HISTORY', EXIST = eof)
IF (.NOT. eof) THEN
PRINT *, "ERROR: cannot find HISTORY file"
STOP
END IF
OPEN (ntraj, file = 'HISTORY', access = 'stream', form = 'unformatted', status = 'unknown')
swapend = .false.
READ (ntraj) endver, Dlen
IF (endver/=endversion) THEN
swapend = .true.
CLOSE (ntraj)
IF (bigend) THEN
OPEN (ntraj, file = 'HISTORY', access = 'stream', form = 'unformatted', status = 'unknown', convert = 'little_endian')
ELSE
OPEN (ntraj, file = 'HISTORY', access = 'stream', form = 'unformatted', status = 'unknown', convert = 'big_endian')
END IF
READ (ntraj) endver, Dlen
IF (endver/=endversion) THEN
PRINT *, "ERROR: corrupted HISTORY file or created with incorrect version of DL_MESO"
STOP
END IF
END IF
IF (Dlen/=lend) THEN
PRINT *, "ERROR: incorrect type of real number used in HISTORY file"
PRINT *, " recompile format_history.f90 with reals of ", Dlen, " bytes"
STOP
END IF
! Open the output file
nform = ntraj + 1
OPEN (nform, file = 'HISTORY'//"-F", status = 'replace')
! read file size, number of frames and timestep numbers
READ (ntraj) filesize, numframe, nstep
! read the number of beads, molecules and bonds
! Arrays are filled with names of particles and molecules: if checking molecules,
! arrays for species, molecule types etc. also filled
READ (ntraj) text
READ (ntraj) nspe, nmoldef, nusyst, nsyst, numbond, keytrj, srfx, srfy, srfz
IF (lcomm) WRITE (nform,*) "# Simulation name:"
WRITE (nform,*) text
IF (lcomm) WRITE (nform,*) "# nspe, nmoldef, nusyst, nsyst, numbond"
WRITE (nform,*) nspe, nmoldef, nusyst, nsyst, numbond
IF (lcomm) WRITE (nform,*) "# keytrj, srfx, srfy, srfz"
WRITE (nform,*) keytrj, srfx, srfy, srfz
framesize = (keytrj+1) * 3
ALLOCATE (namspe (nspe), nammol (nmoldef), globindex (nsyst), readint (nsyst), readdata (framesize))
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))
END IF
IF (lcomm) WRITE (nform,*) "# SPECIES:"
IF (lcomm) WRITE (nform,*) "# namspe, amass, rcii, chge, lfrzn"
DO i = 1, nspe
READ (ntraj) namspe (i), amass, rcii, chge, lfrzn
WRITE (nform,96) namspe (i), amass, rcii, chge, lfrzn
END DO
IF (nmoldef>0) THEN
IF (lcomm) WRITE (nform,*) "# MOLECULES:"
IF (lcomm) WRITE (nform,*) "# nammol"
DO i = 1, nmoldef
READ (ntraj) nammol (i)
WRITE (nform,*) nammol (i)
END DO
END IF
! (if required) read and fill arrays with properties of beads and molecules
nummol = 0 ! counter for number of molecules
IF (lcomm) WRITE (nform,*) "# BEADS:"
IF (lcomm) WRITE (nform,*) "# global, species, molecule, chain"
IF (lmcheck) THEN
! Build ltp, ltm, mole
DO i = 1, nsyst
READ (ntraj) global, species, molecule, chain
ltp (global) = species
ltm (global) = molecule
mole (global) = chain
nummol = MAX (nummol, chain)
WRITE (nform,*) global, species, molecule, chain
END DO
ELSE
DO i = 1, nsyst
READ (ntraj) global, species, molecule, chain
WRITE (nform,*) global, species, molecule, chain
END DO
END IF
IF (numbond>0) THEN
IF (lcomm) WRITE (nform,*) "# BONDS:"
IF (lcomm) WRITE (nform,*) "# extremes of the bond"
IF (lmcheck) THEN
! Build bndtbl
DO i = 1, numbond
READ (ntraj) bead1, bead2
bndtbl (i, 1) = bead1
bndtbl (i, 2) = bead2
WRITE (nform,*) bead1, bead2
END DO
ELSE
DO i = 1, numbond
READ (ntraj) bead1, bead2
WRITE (nform,*) bead1, bead2
END DO
END IF
END IF
! reached end of header: find current position in file
INQUIRE (unit=ntraj, POS=headerpos)
framesizeli = INT (framesize, KIND=li)
numbeadsli = INT (nsyst, KIND=li)
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
! Now read in trajectories
eof = .false.
IF (lcomm) WRITE (nform,*) "# --- TRAJECTORIES --- (key =", keytrj,")"
SELECT CASE (keytrj)
CASE (0)
IF (lcomm) WRITE (nform,*) "# mglobal, x, y, z"
CASE(1)
IF (lcomm) WRITE (nform,*) "# mglobal, x, y, z, vx, vy, vz"
CASE(2)
IF (lcomm) WRITE (nform,*) "# mglobal, x, y, z, vx, vy, vz, fx, fy, fz"
END SELECT
DO k = 1, numframe
currentpos = headerpos + INT (k-1, KIND=li) * ((7_li + numbeadsli * framesizeli) * lend_li + (1_li + numbeadsli) * leni_li)
READ (ntraj, POS=currentpos, IOSTAT=ioerror) time, nbeads, dimx, dimy, dimz, shrdx, shrdy, shrdz
IF (ioerror/=0) THEN
eof = .true.
IF (k==1) THEN
PRINT *, 'ERROR: cannot find trajectory data in HISTORY file'
STOP
END IF
EXIT
END IF
IF (lcomm) WRITE (nform,*) "# time, nbeads, dimx, dimy, dimz, shrdx, shrdy, shrdz"
WRITE (nform,98) time, nbeads, dimx, dimy, dimz, shrdx, shrdy, shrdz
IF (lcomm) WRITE (nform,*) "# snapshot number:", k
IF (sorted) THEN
READ (ntraj) readint (1:nbeads)
CALL quicksort_integer_indexed (readint, 1, nbeads, globindex)
DO i = 1, nbeads
global = globindex (i)
mypos = currentpos + leni_li * (1_li + numbeadsli) + (7_li + INT (global-1, KIND=li) * framesizeli) * lend_li
READ (ntraj, POS=mypos) readdata (1:framesize)
WRITE (nform,99) global, readdata (1:framesize)
END DO
ELSE
READ (ntraj) globindex (1:nbeads)
DO i = 1, nbeads
READ (ntraj, POS=mypos) readdata (1:framesize)
WRITE (nform,99) global, readdata (1:framesize)
END DO
END IF
END DO
! Close the trajectory file
CLOSE (ntraj)
! close the output file
CLOSE (nform)
DEALLOCATE (readint, readdata, globindex)
DEALLOCATE (namspe, nammol)
IF (lmcheck) DEALLOCATE (ltp, ltm, mole, nmol, nbdmol, bndtbl, nbomol)
99 FORMAT(I10,2x,1p,9(e13.6,3x))
98 FORMAT(f10.3,3x,1x,I10,6(f10.3,3x))
96 FORMAT(A9,3x,3(f10.3,3x),I2)
CONTAINS
SUBROUTINE quicksort_integer_indexed (list, stride, n, indices)
!**********************************************************************
!
! sort integers in array into numerical order, recording original
! positions of values (routine to prepare indices array)
!
! copyright ukri stfc daresbury laboratory
! authors - m. a. seaton august 2013
!
!**********************************************************************
INTEGER, INTENT (INOUT) :: list (:)
INTEGER, INTENT (IN) :: stride, n
INTEGER, INTENT (OUT) :: indices (:)
INTEGER :: i
DO i = 1, n
indices (i) = i
END DO
CALL qsort_integer (list, indices, stride, 1, n)
END SUBROUTINE quicksort_integer_indexed
RECURSIVE SUBROUTINE qsort_integer (list, index, stride, low, high)
!**********************************************************************
!
! sort integers in array into numerical order, recording original
! positions of values
!
! copyright ukri stfc daresbury laboratory
! authors - m. a. seaton august 2013
!
!**********************************************************************
INTEGER, INTENT (INOUT) :: list (:), index (:)
INTEGER, INTENT (IN) :: low, high
INTEGER, INTENT (IN) :: stride
INTEGER :: i, j, k, reference, temp
IF (high < low + 6) THEN
! resort to bubble sort for very small lists (5 items or fewer)
DO i = low, high - 1
DO j = i+1, high
IF (list (stride * (i - 1) + 1) > list (stride * (j - 1) + 1)) THEN
DO k = 1, stride
temp = list (stride * (i - 1) + k)
list (stride * (i - 1) + k) = list (stride * (j - 1) + k)
list (stride * (j - 1) + k) = temp
END DO
temp = index (i)
index (i) = index (j)
index (j) = temp
END IF
END DO
END DO
ELSE
! apply partition-based sort
reference = list (stride * ((low+high)/2 - 1) + 1)
i = low - 1
j = high + 1
DO
DO
i = i + 1
IF (list (stride * (i-1) + 1) >= reference) EXIT
END DO
DO
j = j - 1
IF (list (stride * (j-1) + 1) <= reference) EXIT
END DO
IF (i < j) THEN
DO k = 1, stride
temp = list (stride * (i-1) + k)
list (stride * (i-1) + k) = list (stride * (j-1) + k)
list (stride * (j-1) + k) = temp
END DO
temp = index (i)
index (i) = index (j)
index (j) = temp
ELSE IF (i == j) THEN
i = i + 1
EXIT
ELSE
EXIT
END IF
END DO
IF (low<j) CALL qsort_integer (list, index, stride, low, j)
IF (i<high) CALL qsort_integer (list, index, stride, i, high)
END IF
END SUBROUTINE qsort_integer
END PROGRAM format_history
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