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Fix box unit string for velocity dump
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@mkrack
mkrack committed Jun 9, 2020
1 parent 6e0731f commit 26d7c8d
Showing 1 changed file with 66 additions and 64 deletions.
130 changes: 66 additions & 64 deletions src/motion/dumpdcd.F
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

PROGRAM dumpdcd

! Version: 3.0
! Version: 3.1
! Author: Matthias Krack (MK)
! History: - Creation (13.02.2012,MK)
! - XYZ file option added (13.02.2012,MK)
Expand All @@ -20,6 +20,7 @@ PROGRAM dumpdcd
! - 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)
! - Fix box unit string for velocity dump (07.06.2020,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.
Expand Down Expand Up @@ -527,11 +528,12 @@ PROGRAM dumpdcd
! 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))") &
WRITE (UNIT=error_unit, FMT="(A,/,(A,T19,A,F12.6))") &
"#", &
"# a [Angstrom] : ", a, &
"# b [Angstrom] : ", b, &
"# c [Angstrom] : ", c, &
"# a "//TRIM(unit_string), ": ", a, &
"# b "//TRIM(unit_string), ": ", b, &
"# c "//TRIM(unit_string), ": ", c
WRITE (UNIT=error_unit, FMT="(A,F12.6)") &
"# alpha [degree] : ", alpha, &
"# beta [degree] : ", beta, &
"# gamma [degree] : ", gamma
Expand Down Expand Up @@ -848,7 +850,7 @@ SUBROUTINE abort_program(routine, 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 ***"
STOP "*** ABNORMAL PROGRAM TERMINATION of dumpdcd v3.1 ***"

END SUBROUTINE abort_program

Expand Down Expand Up @@ -1120,68 +1122,68 @@ SUBROUTINE print_help()
! Print the program flags for help

WRITE (UNIT=*, FMT="(T2,A)") &
"", &
"Program flags for "//TRIM(version_info)//":", &
"", &
" -debug, -d : Print debug information", &
" -ekin : Dump just the ""temperature"" of each atom", &
" -eformat : Print coordinates in scientific format", &
" -eo : Write standard output and standard error to the same logical unit", &
" -first_frame, -ff <int> : Number of the first frame which is dumped", &
" -help, -h : Print this information", &
" -info, -i : Print additional information for each frame (see also -debug flag)", &
" -last_frame, -lf <int> : Number of the last frame which is dumped", &
" -output, -o <file_name> : Name of the output file (default is stdout)", &
" -output_format, -of <DCD|XMOL> : Output format for dump", &
" -pbc : Apply the periodic boundary conditions (PBC) to each frame before it is dumped", &
" (origin at lower left)", &
" -pbc0 : Apply the periodic boundary conditions (PBC) to each frame before it is dumped", &
" (origin at box centre)", &
" -stride <int> : Stride for frame dump (allows to skip frames, e.g. by dumping each 10th frame)", &
" -trace_atoms <real> : Print the atoms which left the simulation box given a threshold value in scaled units", &
" -vel2cord, -v2c : Dump a VELocity DCD file as COoRDinate DCD file (hack which allows a digest by VMD)", &
" -xyz_file, -xyz <file_name> : Name of a reference XYZ file in XMOL format that provides the atomic labels", &
""
"", &
"Program flags for "//TRIM(version_info)//":", &
"", &
" -debug, -d : Print debug information", &
" -ekin : Dump just the ""temperature"" of each atom", &
" -eformat : Print coordinates in scientific format", &
" -eo : Write standard output and standard error to the same logical unit", &
" -first_frame, -ff <int> : Number of the first frame which is dumped", &
" -help, -h : Print this information", &
" -info, -i : Print additional information for each frame (see also -debug flag)", &
" -last_frame, -lf <int> : Number of the last frame which is dumped", &
" -output, -o <file_name> : Name of the output file (default is stdout)", &
" -output_format, -of <DCD|XMOL> : Output format for dump", &
" -pbc : Apply the periodic boundary conditions (PBC) to each frame before it is dumped", &
" (origin at lower left)", &
" -pbc0 : Apply the periodic boundary conditions (PBC) to each frame before it is dumped", &
" (origin at box centre)", &
" -stride <int> : Stride for frame dump (allows to skip frames, e.g. by dumping each 10th frame)", &
" -trace_atoms <real> : Print the atoms which left the simulation box given a threshold value in scaled units", &
" -vel2cord, -v2c : Dump a VELocity DCD file as COoRDinate DCD file (hack which allows a digest by VMD)", &
" -xyz_file, -xyz <file_name> : Name of a reference XYZ file in XMOL format that provides the atomic labels", &
""

WRITE (UNIT=*, FMT="(T2,A)") &
"Usage examples:", &
"", &
" dumpdcd <optional flags> <DCD file(s)>", &
"", &
"Specific usage examples:", &
"", &
" dumpdcd UO2-2x2x2-pos-1.dcd (without atomic labels from XYZ file)", &
" dumpdcd -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd (single DCD file)", &
" dumpdcd -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd UO2-2x2x2-pos-2.dcd ... (multiple DCD files are dumped consecutively)", &
" dumpdcd -info -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd UO2-2x2x2-pos-2.dcd (print additional information)", &
" dumpdcd -debug -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd UO2-2x2x2-pos-2.dcd (print debug information)", &
" dumpdcd -ekin -d -xyz UO2-2x2x2.xyz UO2-2x2x2-vel-1.dcd (print the ""temperature"" of each atom)", &
" dumpdcd -ekin -xyz UO2-2x2x2.xyz UO2-2x2x2-vel-1.dcd (print just the temperature of each atom)", &
" dumpdcd -first_frame 5 -last_frame 10 UO2-2x2x2-pos-1.dcd (just dump frame 5 to 10, ie. 6 frames in total)", &
" dumpdcd -o outfile.xyz UO2-2x2x2-pos-1.dcd (write output to the file ""outfile.xyz"" instead of stdout)", &
" dumpdcd -o test.xyz -output_format xmol -xyz ref.xyz -first 10 -last 10 test.dcd (dump 10th frame in XMOL format)", &
" dumpdcd -of dcd -ff 10 -lf 20 test.dcd (dump the frames 10 to 20 in DCD format to the default output file output.dcd)", &
" dumpdcd -o part.dcd -of dcd -ff 1 -lf 3 test.dcd (dump the frames 1 to 3 in DCD format to the output file part.dcd)", &
" dumpdcd -o part.dcd -of dcd -first 10 -lf 100 -stride 10 test.dcd (dump the frames 10, 20, ..., 100 to the file part.dcd)", &
" dumpdcd -output new.dcd -output_format dcd -pbc old.dcd (dump all frames applying PBC to the output file new.dcd)", &
" dumpdcd -o new.dcd -of dcd -pbc -trace_atoms 0.02 old.dcd (all atoms more than 2% out of the box are listed)", &
" dumpdcd -o new.dcd -e out_of_box.log -of dcd -pbc -trace_atoms 0.1 old.dcd (atoms more than 10% out of the box are listed)", &
" dumpdcd -o new.dcd -of dcd -vel2cord old.dcd (dump old.dcd as new.dcd and change only the DCD id string from VEL to CORD)", &
" dumpdcd -o new.dcd -of dcd -frc2cord old.dcd (dump old.dcd as new.dcd and change only the DCD id string from FRC to CORD)", &
" dumpdcd -i -disp UO2-2x2x2-pos-1.dcd (dump the displacements of all atoms w.r.t. their positions in the first frame)", &
" dumpdcd -i -of dcd -disp UO2-2x2x2-pos-1.dcd (dump the atomic displacements as x-coordinates of a DCD CORD file)", &
" dumpdcd -i -of dcd -ekin -v2c -xyz UO2-2x2x2.xyz UO2-2x2x2-vel-1.dcd (dump the atomic temperatures as x-coordinates of a ", &
" DCD CORD file -> hack for VMD)", &
""
"Usage examples:", &
"", &
" dumpdcd <optional flags> <DCD file(s)>", &
"", &
"Specific usage examples:", &
"", &
" dumpdcd UO2-2x2x2-pos-1.dcd (without atomic labels from XYZ file)", &
" dumpdcd -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd (single DCD file)", &
" dumpdcd -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd UO2-2x2x2-pos-2.dcd ... (multiple DCD files are dumped consecutively)", &
" dumpdcd -info -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd UO2-2x2x2-pos-2.dcd (print additional information)", &
" dumpdcd -debug -xyz UO2-2x2x2.xyz UO2-2x2x2-pos-1.dcd UO2-2x2x2-pos-2.dcd (print debug information)", &
" dumpdcd -ekin -d -xyz UO2-2x2x2.xyz UO2-2x2x2-vel-1.dcd (print the ""temperature"" of each atom)", &
" dumpdcd -ekin -xyz UO2-2x2x2.xyz UO2-2x2x2-vel-1.dcd (print just the temperature of each atom)", &
" dumpdcd -first_frame 5 -last_frame 10 UO2-2x2x2-pos-1.dcd (just dump frame 5 to 10, ie. 6 frames in total)", &
" dumpdcd -o outfile.xyz UO2-2x2x2-pos-1.dcd (write output to the file ""outfile.xyz"" instead of stdout)", &
" dumpdcd -o test.xyz -output_format xmol -xyz ref.xyz -first 10 -last 10 test.dcd (dump 10th frame in XMOL format)", &
" dumpdcd -of dcd -ff 10 -lf 20 test.dcd (dump the frames 10 to 20 in DCD format to the default output file output.dcd)", &
" dumpdcd -o part.dcd -of dcd -ff 1 -lf 3 test.dcd (dump the frames 1 to 3 in DCD format to the output file part.dcd)", &
" dumpdcd -o part.dcd -of dcd -first 10 -lf 100 -stride 10 test.dcd (dump the frames 10, 20, ..., 100 to the file part.dcd)", &
" dumpdcd -output new.dcd -output_format dcd -pbc old.dcd (dump all frames applying PBC to the output file new.dcd)", &
" dumpdcd -o new.dcd -of dcd -pbc -trace_atoms 0.02 old.dcd (all atoms more than 2% out of the box are listed)", &
" dumpdcd -o new.dcd -e out_of_box.log -of dcd -pbc -trace_atoms 0.1 old.dcd (atoms more than 10% out of the box are listed)", &
" dumpdcd -o new.dcd -of dcd -vel2cord old.dcd (dump old.dcd as new.dcd and change only the DCD id string from VEL to CORD)", &
" dumpdcd -o new.dcd -of dcd -frc2cord old.dcd (dump old.dcd as new.dcd and change only the DCD id string from FRC to CORD)", &
" dumpdcd -i -disp UO2-2x2x2-pos-1.dcd (dump the displacements of all atoms w.r.t. their positions in the first frame)", &
" dumpdcd -i -of dcd -disp UO2-2x2x2-pos-1.dcd (dump the atomic displacements as x-coordinates of a DCD CORD file)", &
" dumpdcd -i -of dcd -ekin -v2c -xyz UO2-2x2x2.xyz UO2-2x2x2-vel-1.dcd (dump the atomic temperatures as x-coordinates of a ", &
" DCD CORD file -> hack for VMD)", &
""

WRITE (UNIT=*, FMT="(T2,A)") &
"Notes:", &
"", &
" - 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", &
""
"Notes:", &
"", &
" - 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", &
""

END SUBROUTINE print_help

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