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dumpdcd.f90
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dumpdcd.f90
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PROGRAM dumpdcd
! Copyright (C) 2012 - 2016 Matthias Krack (MK)
!
! Version: 3.0
! Author: Matthias Krack (MK)
! History: - Creation (13.02.2012,MK)
! - XYZ file option added (13.02.2012,MK)
! - Flags added for first and last frame and -o for output (24.05.2012,MK)
! - XMOL flag added (25.05.2012,MK)
! - PBC flag added (04.06.2012,MK)
! - Stride flag added (05.06.2012,MK)
! - Tracing of atoms added to detect the atoms which left the box (06.06.2012,MK)
! - Keep input coordinates for further processing steps (15.06.2012,MK)
! - VEL to CORD (-vel2cord flag) hack added (25.06.2012,MK)
! - Added -displacement (-disp) flag (26.06.2012,MK)
! - Dump the atomic displacements (CORD file) or temperatures (VEL file as x-coordinates of a DCD file (28.06.2012,MK)
! - FRC to CORD (-frc2cord flag) hack added (28.01.2016,MK)
! - Option -eformat added (15.02.2016,MK)
!
! Note: For -ekin a XYZ file is required to obtain the atomic labels.
! The -info and the -debug flags provide a more detailed output which is especially handy for tracing problems.
! The output in DCD format is in binary format.
! The input coordinates should be in Angstrom. Velocities and forces are expected to be in atomic units.
! Uncomment the following line if this module is available (e.g. with gfortran) and comment the corresponding variable declarations below
! USE ISO_FORTRAN_ENV, ONLY: error_unit,input_unit,output_unit
IMPLICIT NONE
! Comment the following lines if the ISO_FORTRAN_ENV is used (see above)
INTEGER, PARAMETER :: default_error_unit = 0,&
default_input_unit = 5,&
default_output_unit = 6
INTEGER :: error_unit = default_error_unit,&
input_unit = default_input_unit,&
output_unit = default_output_unit
! End Comment
! Parameters
CHARACTER(LEN=*), PARAMETER :: routine_name = "dumpdcd",&
version_info = routine_name//" v3.0 (31.01.2014, Matthias Krack)"
INTEGER, PARAMETER :: dp = SELECTED_REAL_KIND(14,200),&
sp = SELECTED_REAL_KIND(6,30)
INTEGER, PARAMETER :: default_string_length = 240,&
xyz_input_unit = 10
REAL(KIND=dp), PARAMETER :: pi = 3.14159265358979323846264338_dp
REAL(KIND=dp), PARAMETER :: angstrom = 0.52917720859_dp,& ! [a.u.] -> [Angstrom]
degree = 180.0_dp/pi,& ! [rad] -> [degree]
kelvin = 315774.647902944_dp,& ! [a.u.] -> [K]
massunit = 1822.88484264550_dp ! [u] -> [a.u.]
! Variables
CHARACTER(LEN=4) :: id_dcd
CHARACTER(LEN=10) :: unit_string
CHARACTER(LEN=17) :: fmt_string
CHARACTER(LEN=default_string_length) :: arg,dcd_file_name,message,out_file_name,output_format,&
remark_xyz,string,xyz_file_name
CHARACTER(LEN=5), DIMENSION(:), ALLOCATABLE :: atomic_label
CHARACTER(LEN=80), DIMENSION(2) :: remark_dcd
INTEGER :: first_frame,have_unit_cell,i,iarg,&
iatom,iskip,istat,istep,last_frame,narg,&
natom_dcd,natom_xyz,ndcd_file,nframe,&
nframe_read,nremark,stride
LOGICAL :: apply_pbc,debug,dump_frame,eformat,ekin,eo,have_atomic_labels,&
info,opened,output_format_dcd,output_format_xmol,&
pbc0,print_atomic_displacements,print_scaled_coordinates,&
print_scaled_pbc_coordinates,trace_atoms,vel2cord
REAL(KIND=sp) :: dt
REAL(KIND=dp) :: a,alpha,b,beta,c,eps_out_of_box,gamma,tavg,tavg_frame
INTEGER, DIMENSION(16) :: idum
REAL(KIND=dp), DIMENSION(3) :: rdum
REAL(KIND=dp), DIMENSION(:), ALLOCATABLE :: atomic_displacement,atomic_mass,atomic_temperature
REAL(KIND=dp), DIMENSION(3,3) :: h,hinv
REAL(KIND=sp), DIMENSION(:,:), ALLOCATABLE :: r
REAL(KIND=dp), DIMENSION(:,:), ALLOCATABLE :: r_pbc,r0,s,s_pbc
apply_pbc = .FALSE.
pbc0 = .FALSE.
debug = .FALSE.
dump_frame = .TRUE.
eformat = .FALSE.
ekin = .FALSE.
eo = .FALSE.
info = .FALSE.
trace_atoms = .FALSE.
vel2cord = .FALSE.
print_atomic_displacements = .FALSE.
print_scaled_coordinates = .FALSE.
print_scaled_pbc_coordinates = .FALSE.
first_frame = 1
last_frame = 1000000 ! Hard limit of 1 Mio frames in total
stride = 1
ndcd_file = 0
nframe = 0
nframe_read = 0
nremark = 0
have_unit_cell = 0
have_atomic_labels = .FALSE.
idum(:) = 0
rdum(:) = 0.0_dp
id_dcd = ""
dcd_file_name = ""
out_file_name = ""
xyz_file_name = ""
output_format = "default"
output_format_dcd = .FALSE.
output_format_xmol = .FALSE.
remark_dcd(:) = ""
remark_xyz = ""
fmt_string = ""
dt = 0.0_sp
a = 0.0_dp
b = 0.0_dp
c = 0.0_dp
alpha = 0.0_dp
beta = 0.0_dp
gamma = 0.0_dp
eps_out_of_box = -HUGE(0.0_dp)
tavg = 0.0_dp
tavg_frame = 0.0_dp
narg = command_argument_count()
IF (narg == 0) THEN
CALL print_help()
CALL abort_program(routine_name,"No input file(s) specified")
END IF
iarg = 0
dcd_file_loop: DO
iarg = iarg + 1
CALL get_command_argument(NUMBER=iarg,VALUE=arg,STATUS=istat)
SELECT CASE (arg)
CASE ("-debug","-d")
debug = .TRUE.
info = .TRUE.
CYCLE dcd_file_loop
CASE ("-displacements","-disp")
print_atomic_displacements = .TRUE.
CYCLE dcd_file_loop
CASE ("-eformat")
eformat = .TRUE.
CYCLE dcd_file_loop
CASE ("-ekin")
ekin = .TRUE.
CYCLE dcd_file_loop
CASE ("-eo")
eo = .TRUE.
CYCLE dcd_file_loop
CASE ("-first_frame","-first","-ff")
iarg = iarg + 1
CALL get_command_argument(NUMBER=iarg,VALUE=arg,STATUS=istat)
READ (UNIT=arg,FMT=*,ERR=100) first_frame
IF (first_frame <= 0) THEN
CALL abort_program(routine_name,"Invalid number for first frame specified: "//&
"first_frame must be greater than zero")
END IF
CYCLE dcd_file_loop
100 CALL abort_program(routine_name,"Invalid number for first frame specified "//&
"(an integer number greater than zero is expected)")
CASE ("-help","-h")
CALL print_help()
STOP
CASE ("-info","-i")
info = .TRUE.
CYCLE dcd_file_loop
CASE ("-last_frame","-last","-lf")
iarg = iarg + 1
CALL get_command_argument(NUMBER=iarg,VALUE=arg,STATUS=istat)
READ (UNIT=arg,FMT=*,ERR=101) last_frame
IF (last_frame <= 0) THEN
CALL abort_program(routine_name,"Invalid number for last frame specified: "//&
"last_frame must be greater than zero")
END IF
CYCLE dcd_file_loop
101 CALL abort_program(routine_name,"Invalid number for last frame specified "//&
"(an integer number greater than zero is expected)")
CASE ("-o","-output")
iarg = iarg + 1
CALL get_command_argument(NUMBER=iarg,VALUE=out_file_name,STATUS=istat)
CYCLE dcd_file_loop
CASE ("-output_format","-of")
iarg = iarg + 1
CALL get_command_argument(NUMBER=iarg,VALUE=output_format,STATUS=istat)
CALL uppercase(output_format)
SELECT CASE (output_format)
CASE ("DCD")
output_format_dcd = .TRUE.
output_format_xmol = .FALSE.
CASE ("XMOL")
output_format_dcd = .FALSE.
output_format_xmol = .TRUE.
CASE DEFAULT
CALL abort_program(routine_name,"Invalid output format type specified")
END SELECT
CYCLE dcd_file_loop
CASE ("-pbc")
apply_pbc = .TRUE.
pbc0 = .FALSE.
CYCLE dcd_file_loop
CASE ("-pbc0")
apply_pbc = .TRUE.
pbc0 = .TRUE.
CYCLE dcd_file_loop
CASE ("-scaled_coordinates","-sc")
print_scaled_coordinates = .TRUE.
CYCLE dcd_file_loop
CASE ("-scaled_pbc_coordinates","-spc")
print_scaled_pbc_coordinates = .TRUE.
CYCLE dcd_file_loop
CASE ("-stride")
iarg = iarg + 1
CALL get_command_argument(NUMBER=iarg,VALUE=arg,STATUS=istat)
READ (UNIT=arg,FMT=*,ERR=104) stride
IF (stride < 1) THEN
CALL abort_program(routine_name,"Invalid stride for frame dump specified: stride must be greater than zero")
END IF
CYCLE dcd_file_loop
104 CALL abort_program(routine_name,"Invalid stride for frame dump specified "//&
"(an integer number greater than 0 is expected)")
CASE ("-trace_atoms")
iarg = iarg + 1
CALL get_command_argument(NUMBER=iarg,VALUE=arg,STATUS=istat)
READ (UNIT=arg,FMT=*,ERR=108) eps_out_of_box
IF (eps_out_of_box <= 0.0_dp) THEN
CALL abort_program(routine_name,"Invalid threshold value for -trace_atoms flag specified")
END IF
trace_atoms = .TRUE.
CYCLE dcd_file_loop
108 CALL abort_program(routine_name,"Invalid threshold value for -trace_atoms flag specified")
CASE ("-vel2cord","-v2c","-frc2cord","-f2c")
vel2cord = .TRUE.
CYCLE dcd_file_loop
CASE ("-xyz","xyz_file")
iarg = iarg + 1
CALL get_command_argument(NUMBER=iarg,VALUE=xyz_file_name,STATUS=istat)
have_atomic_labels = .TRUE.
CYCLE dcd_file_loop
CASE DEFAULT
IF (arg(1:1) == "-") THEN
CALL print_help()
CALL abort_program(routine_name,"Unknown command line flag """//TRIM(arg)//""" found")
END IF
dcd_file_name = arg
END SELECT
! Check flag compatibility
IF (first_frame > last_frame) THEN
CALL abort_program(routine_name,"Number of first frame greater than number of last frame")
END IF
IF ((.NOT.have_atomic_labels).AND.output_format_xmol) THEN
CALL abort_program(routine_name,"The output format XMOL requires a valid xyz file (-xyz flag)")
END IF
IF (output_format_xmol.AND.ekin) THEN
CALL abort_program(routine_name,"Output format XMOL and the -ekin flag are incompatible")
END IF
IF (output_format_xmol.AND.print_atomic_displacements) THEN
CALL abort_program(routine_name,"Output format XMOL and the -displacements flag are incompatible")
END IF
IF (output_format_xmol.AND.eo) THEN
CALL abort_program(routine_name,"The -eo flag is incompatible with the output format XMOL")
END IF
IF (.NOT.have_atomic_labels.AND.ekin) THEN
CALL abort_program(routine_name,"ekin flag requires also the specification of a valid xyz file (-xyz flag)")
END IF
IF (.NOT.apply_pbc.AND.trace_atoms) THEN
CALL abort_program(routine_name,"The -trace_atoms flag requires the specification of a -pbc flag")
END IF
IF (ekin.AND.print_atomic_displacements) THEN
CALL abort_program(routine_name,"The -ekin flag and the -displacements flag are incompatible")
END IF
IF (print_scaled_coordinates.AND.print_scaled_pbc_coordinates) THEN
CALL abort_program(routine_name,"The -sc flag and the -spc flag are incompatible")
END IF
IF (.NOT.apply_pbc.AND.print_scaled_coordinates) THEN
CALL abort_program(routine_name,"The -sc flag requires the specification of a -pbc flag")
END IF
IF (.NOT.apply_pbc.AND.print_scaled_pbc_coordinates) THEN
CALL abort_program(routine_name,"The -spc flag requires the specification of a -pbc flag")
END IF
! Use optionally an ES format
IF (eformat) THEN
fmt_string = "(A5,3(1X,ES14.6))"
ELSE
fmt_string = "(A5,3(1X, F14.6))"
END IF
! Open output units as requested
IF (output_format_dcd) THEN
! Set default output file name if no file name was specified
IF (LEN_TRIM(out_file_name) == 0) out_file_name = "output.dcd"
! Check if a new output file name was specified, if yes then close the old unit
INQUIRE (UNIT=output_unit,NAME=string)
IF (TRIM(string) /= TRIM(out_file_name)) CLOSE (UNIT=output_unit)
INQUIRE (UNIT=output_unit,OPENED=opened)
IF (.NOT.opened) THEN
OPEN (UNIT=output_unit,&
FILE=out_file_name,&
STATUS="UNKNOWN",&
ACCESS="SEQUENTIAL",&
FORM="UNFORMATTED",&
ACTION="WRITE",&
IOSTAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"The unformatted output file could not be opened")
END IF
ELSE
IF (eo) error_unit = output_unit
IF (LEN_TRIM(out_file_name) > 0) THEN
! Check if a new output file name was specified, if yes then close the old unit
INQUIRE (UNIT=output_unit,NAME=string)
IF (TRIM(string) /= TRIM(out_file_name)) CLOSE (UNIT=output_unit)
INQUIRE (UNIT=output_unit,OPENED=opened)
IF (.NOT.opened) THEN
OPEN (UNIT=output_unit,&
FILE=out_file_name,&
STATUS="UNKNOWN",&
ACCESS="SEQUENTIAL",&
FORM="FORMATTED",&
POSITION="REWIND",&
ACTION="WRITE",&
IOSTAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"The formatted output file could not be opened")
END IF
END IF
END IF
! Avoid reading from and writing to the same file
IF (TRIM(dcd_file_name) == TRIM(out_file_name)) THEN
CALL abort_program(routine_name,"Input and output file name cannot be the same")
END IF
! Read reference xyz input file if requested
IF (have_atomic_labels) THEN
string = ""
! Check if a new XYZ input file name was specified, if yes then close the old unit
INQUIRE (UNIT=xyz_input_unit,NAME=string)
IF (TRIM(string) /= TRIM(xyz_file_name)) CLOSE (UNIT=xyz_input_unit)
INQUIRE (UNIT=xyz_input_unit,OPENED=opened)
! Read new XYZ input file if needed and update reference information
IF (.NOT.opened) THEN
OPEN (UNIT=xyz_input_unit,&
FILE=xyz_file_name,&
STATUS="OLD",&
ACCESS="SEQUENTIAL",&
FORM="FORMATTED",&
POSITION="REWIND",&
ACTION="READ",&
IOSTAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"The XYZ file could not be opened")
IF (info) WRITE (UNIT=error_unit,FMT="(A)") "#","# Reading XYZ file: "//TRIM(xyz_file_name)
READ (UNIT=xyz_input_unit,FMT="(A)",IOSTAT=istat) arg
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Reading line 1 of the XYZ file (number of atoms) failed")
END IF
IF (arg(1:1) == "#") THEN
READ (UNIT=arg,FMT=*,IOSTAT=istat) string,natom_xyz
ELSE
READ (UNIT=arg,FMT=*,IOSTAT=istat) natom_xyz
END IF
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Reading line 1 of the XYZ file (number of atoms) failed")
END IF
IF (ALLOCATED(atomic_label)) THEN
DEALLOCATE (atomic_label,STAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"Deallocation of the vector atomic_label failed")
END IF
ALLOCATE (atomic_label(natom_xyz),STAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"Allocation of the vector atomic_label failed")
atomic_label(:) = ""
IF (ekin) THEN
IF (ALLOCATED(atomic_mass)) THEN
DEALLOCATE (atomic_mass,STAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"Deallocation of the vector atomic_mass failed")
END IF
ALLOCATE (atomic_mass(natom_xyz),STAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"Allocation of the vector atomic_mass failed")
END IF
READ (UNIT=xyz_input_unit,FMT="(A)",IOSTAT=istat) remark_xyz
IF (istat /= 0) CALL abort_program(routine_name,"Reading line 2 of the XYZ file (remark line) failed")
iatom = 0
DO
READ (UNIT=xyz_input_unit,FMT=*,IOSTAT=istat) arg
IF (arg(1:1) == "#") THEN
CYCLE
ELSE
BACKSPACE (UNIT=xyz_input_unit)
END IF
iatom = iatom + 1
READ (UNIT=xyz_input_unit,FMT=*,IOSTAT=istat) atomic_label(iatom),rdum(1:3)
IF (istat /= 0) THEN
message = ""
WRITE (UNIT=message,FMT="(A,I0,A,I0,A)")&
"Reading line ",iatom+2," of the XYZ file (atom ",iatom,") failed"
CALL abort_program(routine_name,TRIM(message))
END IF
CALL uppercase(atomic_label(iatom))
IF (LEN_TRIM(atomic_label(iatom)) > 1) CALL lowercase(atomic_label(iatom)(2:2))
atomic_label(iatom) = TRIM(ADJUSTL(atomic_label(iatom)))
IF (ekin) atomic_mass(iatom) = get_atomic_mass(atomic_label(iatom))
IF (iatom == natom_xyz) EXIT
END DO
IF (info) THEN
WRITE (UNIT=error_unit,FMT="(A,I0)")&
"# Number of atoms : ",natom_xyz,&
"# Remark : "//TRIM(ADJUSTL(remark_xyz))
END IF
END IF
END IF
! Increment DCD file counter
ndcd_file = ndcd_file + 1
! Open input file in DCD format
OPEN (UNIT=input_unit,&
FILE=dcd_file_name,&
STATUS="OLD",&
FORM="UNFORMATTED",&
POSITION="REWIND",&
ACTION="READ",&
IOSTAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"The DCD file could not be opened")
IF (info) THEN
WRITE (UNIT=error_unit,FMT="(A,/,(A,I0))")&
"#",&
"# DCD file number : ",ndcd_file,&
"# Reading DCD file: "//TRIM(dcd_file_name)
END IF
! Read 1st record of DCD file
READ (UNIT=input_unit) id_dcd,idum(1),istep,iskip,idum(2:7),dt,have_unit_cell,idum(8:16)
IF (info) THEN
WRITE (UNIT=error_unit,FMT="(A,2(/,A,I0),/,A,F9.3,/,A,I0)")&
"# DCD id string : "//id_dcd,&
"# Step : ",istep,&
"# Print frequency : ",iskip,&
"# Time step [fs] : ",dt,&
"# Unit cell : ",have_unit_cell
END IF
IF (ekin.AND.TRIM(ADJUSTL(id_dcd)) /= "VEL") THEN
CALL abort_program(routine_name,"ekin flag requires a DCD file with VELocities")
END IF
IF (apply_pbc.AND.(have_unit_cell /= 1)) THEN
CALL abort_program(routine_name,"pbc flags require that unit cell information is available")
END IF
IF ((TRIM(ADJUSTL(id_dcd)) == "FRC").OR.(TRIM(ADJUSTL(id_dcd)) == "VEL")) THEN
unit_string = "[a.u.]"
IF (apply_pbc) CALL abort_program(routine_name,"pbc flags require a DCD file with COoRDinates")
ELSE IF (TRIM(ADJUSTL(id_dcd)) == "CORD") THEN
unit_string = "[Angstrom]"
ELSE
CALL abort_program(routine_name,"Unknown DCD id found (use -debug or -info flag for details)")
END IF
! Read 2nd record of DCD file
READ (UNIT=input_unit) nremark,remark_dcd(1),remark_dcd(2)
IF (info) THEN
DO i=1,nremark
WRITE (UNIT=error_unit,FMT="(A,I1,A)")&
"# Remark ",i," : "//TRIM(remark_dcd(i))
END DO
END IF
! Read 3rd record of DCD file
READ (UNIT=input_unit) natom_dcd
IF (info) THEN
WRITE (UNIT=error_unit,FMT="(A,I0)")&
"# Number of atoms : ",natom_dcd
END IF
IF (have_atomic_labels) THEN
IF (natom_dcd /= natom_xyz) CALL abort_program(routine_name,"Number of atoms in XYZ and DCD file differ")
ELSE
IF (.NOT.ALLOCATED(atomic_label)) THEN
ALLOCATE (atomic_label(natom_dcd),STAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"Allocation of the vector atomic_label failed")
atomic_label(:) = ""
END IF
END IF
! Dump output in DCD format => dcd2dcd functionality
IF (output_format_dcd) THEN
IF (vel2cord) id_dcd = "CORD"
! Note, dt is REAL*4 and the rest is INTEGER*4
WRITE (UNIT=output_unit) id_dcd,idum(1),istep,iskip,idum(2:7),dt,have_unit_cell,idum(8:16)
WRITE (UNIT=output_unit) nremark,remark_dcd(1),remark_dcd(2)
WRITE (UNIT=output_unit) natom_dcd
END IF
frame_loop: DO
nframe = nframe + 1
IF (nframe < first_frame) THEN
dump_frame = .FALSE.
ELSE
IF (MODULO(nframe-first_frame,stride) == 0) THEN
dump_frame = .TRUE.
ELSE
dump_frame = .FALSE.
END IF
END IF
! Read unit cell information, if available
IF (have_unit_cell == 1) THEN
READ (UNIT=input_unit,IOSTAT=istat) a,gamma,b,beta,alpha,c
IF (istat < 0) EXIT frame_loop
END IF
IF ((info.OR.trace_atoms).AND.dump_frame) THEN
WRITE (UNIT=error_unit,FMT="(A,/,A,I0)")&
"#","# Frame number : ",nframe
END IF
! Print unit cell information, if available
IF (info.AND.dump_frame) THEN
IF (have_unit_cell == 1) THEN
WRITE (UNIT=error_unit,FMT="(A,/,(A,F12.6))")&
"#",&
"# a [Angstrom] : ",a,&
"# b [Angstrom] : ",b,&
"# c [Angstrom] : ",c,&
"# alpha [degree] : ",alpha,&
"# beta [degree] : ",beta,&
"# gamma [degree] : ",gamma
END IF
END IF
! Allocate the array for the current atomic positions if needed
IF (.NOT.ALLOCATED(r)) THEN
ALLOCATE (r(natom_dcd,3),STAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"Allocation of the array r failed")
END IF
! Read in the atomic positions of the current frame
READ (UNIT=input_unit,IOSTAT=istat) r(1:natom_dcd,1)
IF (istat < 0) EXIT frame_loop
READ (UNIT=input_unit) r(1:natom_dcd,2)
READ (UNIT=input_unit) r(1:natom_dcd,3)
! Store the atomic positions of the first frame in the current DCD input file for
! the output of the atomic displacements
IF ((nframe == 1).AND.print_atomic_displacements) THEN
IF (.NOT.ALLOCATED(r0)) THEN
ALLOCATE (r0(natom_dcd,3),STAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"Allocation of the array r0 failed")
END IF
r0(:,:) = r(:,:)
IF (.NOT.ALLOCATED(atomic_displacement)) THEN
ALLOCATE (atomic_displacement(natom_dcd),STAT=istat)
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Allocation of the vector atomic_displacement failed")
END IF
END IF
atomic_displacement(:) = 0.0_dp
END IF
IF (ekin.AND.TRIM(ADJUSTL(id_dcd)) == "VEL") THEN
! Dump the kinetic energy of each as an "atomic temperature"
IF (dump_frame) THEN
IF (.NOT.ALLOCATED(atomic_temperature)) THEN
ALLOCATE (atomic_temperature(natom_dcd),STAT=istat)
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Allocation of the vector atomic_temperature failed")
END IF
atomic_temperature(:) = 0.0_dp
END IF
IF (info) THEN
WRITE (UNIT=error_unit,FMT="(A)")&
"#",&
"# Temperature [K]"
END IF
tavg_frame = 0.0_dp
DO iatom=1,natom_dcd
atomic_temperature(iatom) = atomic_mass(iatom)*(r(iatom,1)*r(iatom,1) +&
r(iatom,2)*r(iatom,2) +&
r(iatom,3)*r(iatom,3))*kelvin/3.0_dp
tavg_frame = tavg_frame + atomic_temperature(iatom)
END DO
tavg_frame = tavg_frame/REAL(natom_dcd,KIND=dp)
IF (output_format_dcd) THEN
IF (have_unit_cell == 1) THEN
WRITE (UNIT=output_unit) a,gamma,b,beta,alpha,c
END IF
! This is a hack for VMD: dump the atomic temperatures as the x-coordinates
! of a DCD VEL file
WRITE (UNIT=output_unit) REAL(atomic_temperature(:),KIND=sp)
! The y and z coordinates are filled with zeros
atomic_temperature(:) = 0.0_dp
WRITE (UNIT=output_unit) REAL(atomic_temperature(:),KIND=sp)
WRITE (UNIT=output_unit) REAL(atomic_temperature(:),KIND=sp)
ELSE
DO iatom=1,natom_dcd
WRITE (UNIT=output_unit,FMT="(A5,5X,F25.3)") ADJUSTL(atomic_label(iatom)),atomic_temperature
END DO
END IF
IF (info) THEN
WRITE (UNIT=error_unit,FMT="(A,F12.3)")&
"# T [K] this frame: ",tavg_frame
END IF
tavg = tavg + tavg_frame
END IF ! dump_frame
ELSE
IF (dump_frame) THEN
! Apply periodic boundary conditions before dumping the coordinates if requested
IF (apply_pbc) THEN
IF (.NOT.ALLOCATED(r_pbc)) THEN
ALLOCATE (r_pbc(natom_dcd,3),STAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"Allocation of the array r_pbc failed")
END IF
IF (.NOT.ALLOCATED(s)) THEN
ALLOCATE (s(natom_dcd,3),STAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"Allocation of the array s failed")
END IF
IF (.NOT.ALLOCATED(s_pbc)) THEN
ALLOCATE (s_pbc(natom_dcd,3),STAT=istat)
IF (istat /= 0) CALL abort_program(routine_name,"Allocation of the array s_pbc failed")
END IF
CALL pbc(r,r_pbc,s,s_pbc,a,b,c,alpha,beta,gamma,debug,info,pbc0,h,hinv)
CALL write_out_of_box_atoms(atomic_label,r,s,eps_out_of_box,h)
! Overwrite input coordinate with the PBCed coordinates for printing
r(:,:) = REAL(r_pbc(:,:),KIND=sp)
END IF ! apply_pbc
! Calculate the atomic displacements with respect to the first frame,
! i.e. set of atomic positions
IF (print_atomic_displacements) THEN
DO iatom=1,natom_dcd
atomic_displacement(iatom) = SQRT((r(iatom,1) - r0(iatom,1))**2 +&
(r(iatom,2) - r0(iatom,2))**2 +&
(r(iatom,3) - r0(iatom,3))**2)
END DO
END IF
! Dump the atomic coordinates in DCD or XMOL/MOLDEN format
IF (output_format_dcd) THEN
IF (have_unit_cell == 1) THEN
WRITE (UNIT=output_unit) a,gamma,b,beta,alpha,c
END IF
IF (print_atomic_displacements) THEN
! This is a hack for VMD: dump the atomic displacements as the x-coordinates
! of a DCD CORD file
WRITE (UNIT=output_unit) REAL(atomic_displacement(:),KIND=sp)
! The y and z coordinates are filled with zeros
atomic_displacement(:) = 0.0_dp
WRITE (UNIT=output_unit) REAL(atomic_displacement(:),KIND=sp)
WRITE (UNIT=output_unit) REAL(atomic_displacement(:),KIND=sp)
ELSE
! Dump DCD file information
DO i=1,3
WRITE (UNIT=output_unit) r(:,i)
END DO
END IF
ELSE
IF (print_atomic_displacements) THEN
IF (info) THEN
WRITE (UNIT=error_unit,FMT="(A,2(/,A),T15,A)")&
"#",&
"# Displacements :",&
"# "//TRIM(unit_string),"|r|"
END IF
IF (have_atomic_labels) THEN
DO iatom=1,natom_dcd
WRITE (UNIT=output_unit,FMT="(A5,5X,F25.6)") ADJUSTL(atomic_label(iatom)),atomic_displacement(iatom)
END DO
ELSE
DO iatom=1,natom_dcd
WRITE (UNIT=output_unit,FMT="(10X,F25.6)") atomic_displacement(iatom)
END DO
END IF
ELSE
IF (output_format_xmol) THEN
WRITE (UNIT=output_unit,FMT="(T2,I0,/,A,2(I0,A))")&
natom_dcd,"Frame: ",nframe_read + 1,", Step: ",nframe,", "//TRIM(remark_xyz)
DO iatom=1,natom_dcd
WRITE (UNIT=output_unit,FMT=fmt_string) ADJUSTL(atomic_label(iatom)),r(iatom,1:3)
END DO
ELSE
IF (info) THEN
WRITE (UNIT=error_unit,FMT="(A,T20,A)")&
"# "//TRIM(unit_string),"x y z"
END IF
IF (print_scaled_coordinates) THEN
DO iatom=1,natom_dcd
WRITE (UNIT=output_unit,FMT=fmt_string) ADJUSTL(atomic_label(iatom)),s(iatom,1:3)
END DO
ELSE IF (print_scaled_pbc_coordinates) THEN
DO iatom=1,natom_dcd
WRITE (UNIT=output_unit,FMT=fmt_string) ADJUSTL(atomic_label(iatom)),s_pbc(iatom,1:3)
END DO
ELSE
DO iatom=1,natom_dcd
WRITE (UNIT=output_unit,FMT=fmt_string) ADJUSTL(atomic_label(iatom)),r(iatom,1:3)
END DO
END IF
END IF
END IF
END IF ! output_format_dcd
END IF ! dump_frame
END IF
IF (dump_frame) nframe_read = nframe_read + 1
! Exit loop and stop processing, if the last (requested) frame was encountered
IF (nframe >= last_frame) THEN
nframe = nframe - 1
CLOSE (UNIT=input_unit)
EXIT dcd_file_loop
END IF
END DO frame_loop
nframe = nframe - 1
CLOSE (UNIT=input_unit)
IF (iarg >= narg) EXIT dcd_file_loop
END DO dcd_file_loop
IF (info) THEN
WRITE (UNIT=error_unit,FMT="(A,/,A,I0)")&
"#",&
"# Frames processed: ",nframe_read
END IF
IF (ekin.AND.TRIM(ADJUSTL(id_dcd)) == "VEL") THEN
IF (info) THEN
WRITE (UNIT=error_unit,FMT="(A,/,A,F12.3)")&
"#",&
"# T [K] all frames: ",tavg/REAL(nframe_read,KIND=dp)
END IF
END IF
! Print version information
IF (info) THEN
WRITE (UNIT=error_unit,FMT="(A)")&
"#",&
"# Normal termination of "//TRIM(version_info)
END IF
! Close files
IF (have_atomic_labels) CLOSE (UNIT=xyz_input_unit)
IF (LEN_TRIM(out_file_name) > 0) CLOSE (UNIT=output_unit)
! Cleanup
IF (ALLOCATED(atomic_label)) THEN
DEALLOCATE (atomic_label,STAT=istat)
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Deallocation of the vector atomic_label failed")
END IF
END IF
IF (ALLOCATED(atomic_displacement)) THEN
DEALLOCATE (atomic_displacement,STAT=istat)
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Deallocation of the vector atomic_displacement failed")
END IF
END IF
IF (ALLOCATED(atomic_mass)) THEN
DEALLOCATE (atomic_mass,STAT=istat)
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Deallocation of the vector atomic_mass failed")
END IF
END IF
IF (ALLOCATED(atomic_temperature)) THEN
DEALLOCATE (atomic_temperature,STAT=istat)
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Deallocation of the vector atomic_temperature failed")
END IF
END IF
IF (ALLOCATED(r)) THEN
DEALLOCATE (r,STAT=istat)
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Deallocation of the array r failed")
END IF
END IF
IF (ALLOCATED(r0)) THEN
DEALLOCATE (r0,STAT=istat)
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Deallocation of the array r0 failed")
END IF
END IF
IF (ALLOCATED(r_pbc)) THEN
DEALLOCATE (r_pbc,STAT=istat)
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Deallocation of the array r_pbc failed")
END IF
END IF
IF (ALLOCATED(s)) THEN
DEALLOCATE (s,STAT=istat)
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Deallocation of the array s failed")
END IF
END IF
IF (ALLOCATED(s_pbc)) THEN
DEALLOCATE (s_pbc,STAT=istat)
IF (istat /= 0) THEN
CALL abort_program(routine_name,"Deallocation of the array s_pbc failed")
END IF
END IF
CONTAINS
SUBROUTINE abort_program(routine,message)
! Abort the program after printing an error message to stderr
IMPLICIT NONE
CHARACTER(LEN=*), INTENT(IN) :: routine,message
CHARACTER(LEN=2*default_string_length) :: error_message
error_message = "*** ERROR in "//TRIM(routine)//": "//TRIM(message)//" ***"
WRITE (UNIT=default_error_unit,FMT="(/,A,/)") TRIM(error_message)
STOP "*** ABNORMAL PROGRAM TERMINATION of dumpdcd v3.0 ***"
END SUBROUTINE abort_program
SUBROUTINE build_h_matrix(a,b,c,alpha,beta,gamma,h)
! Calculate the h matrix of a simulation cell given the cell edge lengths a, b,
! and c in Angstrom and the angles alpha (<b,c)), beta (<(a,c)), and gamma (<(a,b))
! in degree.
IMPLICIT NONE
CHARACTER(LEN=*), PARAMETER :: routine_name = "build_h_matrix"
REAL(KIND=dp), INTENT(IN) :: a,alpha,b,beta,c,gamma
REAL(KIND=dp), DIMENSION(3,3), INTENT(OUT) :: h
REAL(KIND=dp) :: cosa,cosb,cosg,sing
cosa = COS(alpha/degree)
IF (ABS(cosa) < EPSILON(0.0_dp)) cosa = 0.0_dp
cosb = COS(beta/degree)
IF (ABS(cosb) < EPSILON(0.0_dp)) cosb = 0.0_dp
cosg = COS(gamma/degree)
IF (ABS(cosg) < EPSILON(0.0_dp)) cosg = 0.0_dp
sing = SIN(gamma/degree)
IF (ABS(sing) < EPSILON(0.0_dp)) sing = 0.0_dp
h(1,1) = 1.0_dp
h(2,1) = 0.0_dp
h(3,1) = 0.0_dp
h(1,2) = cosg
h(2,2) = sing
h(3,2) = 0.0_dp
h(1,3) = cosb
h(2,3) = (cosa - cosg*cosb)/sing
IF ((1.0_dp - h(1,3)**2 - h(2,3)**2) < 0.0_dp) THEN
CALL abort_program(routine_name,"Build of the h matrix failed, check cell information")
END IF
h(3,3) = SQRT(1.0_dp - h(1,3)**2 - h(2,3)**2)
h(:,1) = a*h(:,1)
h(:,2) = b*h(:,2)
h(:,3) = c*h(:,3)
END SUBROUTINE build_h_matrix
FUNCTION det_3x3(a) RESULT(det_a)
! Returns the determinante of the 3x3 matrix a.
IMPLICIT NONE
REAL(KIND=dp), DIMENSION(3,3), INTENT(IN) :: a
REAL(KIND=dp) :: det_a
det_a = a(1,1)*(a(2,2)*a(3,3) - a(2,3)*a(3,2)) +&
a(1,2)*(a(2,3)*a(3,1) - a(2,1)*a(3,3)) +&
a(1,3)*(a(2,1)*a(3,2) - a(2,2)*a(3,1))
END FUNCTION det_3x3
FUNCTION get_atomic_mass(element_symbol) RESULT(amass)
! Get the atomic mass amass for an element
IMPLICIT NONE
CHARACTER(LEN=*), INTENT(IN) :: element_symbol
CHARACTER(LEN=*), PARAMETER :: routine_name = "get_atomic_mass"
REAL(KIND=dp) :: amass
SELECT CASE (TRIM(element_symbol))
CASE ("O ")
amass = 15.9994_dp
CASE ("U ")
amass = 238.02891_dp
CASE DEFAULT
CALL abort_program(routine_name,"Unknown element symbol found")
END SELECT
amass = amass*massunit
END FUNCTION get_atomic_mass
SUBROUTINE invert_matrix_3x3(h,hinv,deth)
! Calculate the inverse hinv and the determinant deth of the 3x3 matrix h.
IMPLICIT NONE
REAL(KIND=dp), DIMENSION(3,3), INTENT(IN) :: h
REAL(KIND=dp), DIMENSION(3,3), INTENT(OUT) :: hinv
REAL(KIND=dp), INTENT(OUT) :: deth
CHARACTER(LEN=*), PARAMETER :: routine_name = "invert_matrix_3x3"
deth = det_3x3(h)
! Numerics
deth = ABS(deth)
IF (deth < 1.0E-10_dp) THEN
CALL abort_program(routine_name,"Invalid h matrix for cell found; det(h) < 1.0E-10")
END IF
hinv(1,1) = (h(2,2)*h(3,3) - h(3,2)*h(2,3))/deth
hinv(2,1) = (h(2,3)*h(3,1) - h(3,3)*h(2,1))/deth
hinv(3,1) = (h(2,1)*h(3,2) - h(3,1)*h(2,2))/deth
hinv(1,2) = (h(1,3)*h(3,2) - h(3,3)*h(1,2))/deth
hinv(2,2) = (h(1,1)*h(3,3) - h(3,1)*h(1,3))/deth
hinv(3,2) = (h(1,2)*h(3,1) - h(3,2)*h(1,1))/deth
hinv(1,3) = (h(1,2)*h(2,3) - h(2,2)*h(1,3))/deth
hinv(2,3) = (h(1,3)*h(2,1) - h(2,3)*h(1,1))/deth
hinv(3,3) = (h(1,1)*h(2,2) - h(2,1)*h(1,2))/deth
END SUBROUTINE invert_matrix_3x3
SUBROUTINE lowercase(string)
! Convert all letters in a string to lowercase
CHARACTER(LEN=*), INTENT(INOUT) :: string
INTEGER :: i, iascii
DO i=1,LEN_TRIM(string)
iascii = ICHAR(string(i:i))
IF ((iascii >= 65).AND.(iascii <= 90)) THEN
string(i:i) = CHAR(iascii + 32)
END IF
END DO
END SUBROUTINE lowercase
SUBROUTINE pbc(r,r_pbc,s,s_pbc,a,b,c,alpha,beta,gamma,debug,info,pbc0,h,hinv)
! Apply the periodic boundary conditions (PBC) to the Cartesian coordinate array
! r given the cell edge lengths a, b, and c in Angstrom and the angles alpha (<b,c)),
! beta (<(a,c)), and gamma (<(a,b)) in degree.
! On output r_pbc is updated with the "PBCed" input coordinates, s with the scaled
! input coordinates, and s_pbc with scaled "PBCed" coordinates.
! If pbc0 is true then fold to the range [-l/2,+l/2[ (origin at box centre) else fold
! to the range [0,l[ (origin at lower left box corner).
IMPLICIT NONE
REAL(KIND=sp), DIMENSION(:,:), INTENT(IN) :: r
REAL(KIND=dp), DIMENSION(:,:), INTENT(OUT) :: r_pbc,s,s_pbc
REAL(KIND=dp), INTENT(IN) :: a,alpha,b,beta,c,gamma
LOGICAL, INTENT(IN) :: debug,info,pbc0
REAL(KIND=dp), DIMENSION(3,3), INTENT(OUT) :: h,hinv
CHARACTER(LEN=*), PARAMETER :: routine_name = "pbc"