#!/bin/bash # # Copyright (C) 2007- Angelo Simone (TU Delft) # Licensed under the GNU LGPL Version 2.1 # # Script for generating an XML file with a collection of vtu files. # This XML file can be used by Paraview to generate an animation. # # # Created on 20070905 # Last revision by Jeremy CHU VAN on 20110708 # # Report bugs to a.simone@tudelft.nl # ############################################# # # -- usage string and function usagestr="\n NAME\n \tmakePvd - generate a PVD XML file from a collection of VTU or VTP files\n \tto allow the files to be animated in paraview.\n \n \n SYNOPSIS\n \tmakePvd [NPROC] basename [STEP] output.pvd \n \n \n \tNPROC: number of processes in a parallel computation \n \tSTEP : single step number (if not specified we deal with all available ones)\n \n \n TYPICAL USAGE EXAMPLES\n \n \n \tAssuming that the oomph-lib output files (in tecplot format) have been \n \tconverted to vtu (or vtp) files (using the oomph-convert script), pvd \n \tfiles can be created as follows: \n\n \n \tData from serial computations: \n \t------------------------------ \n \n \t For data files from a serial computation where separate files\n \t represent, e.g., results at different time steps, where the filenames\n \t have the format such as \n\n \t \t plot001.vtu \n \t \t plot002.vtu \n \t \t plot003.vtu \n \t \t \t : \n \n \t \t plot009.vtu \n \t \t plot010.vtu \n \t \t plot011.vtu \n \t \t \t : \n \n \t (i.e. a stem, (here \"plot\"), followed by a padded number \n \t and the \".vtu\" suffix), the pvd file can be generated with \n\n \t \t makePvd [stem] myplot.pvd \n\n \t So for the files listed above we would use the command\n\n \t \t makePvd plot myplot.pvd \n\n \t which generates the file myplot.pvd\n \v \tNote that the numbers do not have to be padded, so files whose names \n \thave the format\n\n \t \t plot1.vtu \n \t \t plot2.vtu \n \t \t plot3.vtu \n \t \t \t : \n \n \t \t plot9.vtu \n \t \t plot10.vtu \n \t \t plot11.vtu \n \t \t \t : \n \n \t can be processed using the same command as above. However, \n \t the combined pvd file will then contain the data in lexicographic\n \t order (e.g. plot1.vtu, plot10.vtu, plot11.vtu, ..., plot19.vtu,\n \t plot2.vtu, plot20.vtu , plot21.vtu, ...) which is likely to create\n \t an odd animation... To create vtu files with padded enumeration \n \t from non-padded data files, use the -z option in the oomph-convert \n \t script. \n \n \n \tData from parallel computations (multiple timesteps): \n \t-----------------------------------------------------\n \n \t oomph-lib typically outputs results from parallel (distributed) \n \t computations on a processor-by-processor basis, resulting in filenames \n \t of the form\n\n \t solid_soln_proc0_00000.vtu \t \t \ \n \t solid_soln_proc1_00000.vtu \t \t | \n \t \t : \t \t \t \t | Data for timestep 0 \n \t solid_soln_proc[NPROC-1]_00000.vtu \t / \n \t \t \n \n \t solid_soln_proc0_00001.vtu \t \t \ \n \t solid_soln_proc1_00001.vtu \t \t | \n \t \t : \t \t \t \t | Data for timestep 1 \n \t solid_soln_proc[NPROC-1]_00001.vtu, \t /\n \n \t \t : \n \n \t where NPROC is the number of processors. An animation of such data \n \t obviously requires the output from different processors (but for the \n \t the same timestep) to be combined. Provided, the filenames have \n \t the pattern \n \n \t \t [stem]proc[processor_number]_[timestep_number].vtu \n\n \t (note the \"proc\" and \"_\", both of which are required), the pvd file \n \t can be generated with \n \n \t \t makePvd [NPROC] [stem] myplot.pvd \n\n \t So, for the files listed above, to produce a pvd file that \n \t contains data from a computation with four processors the command\n\n \t \t makePvd 4 solid_soln_ solid_soln.pvd \n\n \t would create the file solid_soln.pvd from which paraview \n \t can create an animation of the solution. \n \n \n \tData from parallel computations (single timestep/solution): \n \t-----------------------------------------------------------\n \t Finally, we offer the option to combine the parallel data files \n \t for a single timestep (or a single solution) into a single pvd file. \n \t Provided, the filenames have the pattern \n \n \t \t [stem]proc[processor_number]_[timestep_number].vtu \n\n \t (note the \"proc\" and \"_\", both of which are required), the pvd file \n \t can be generated with \n \n \t \t makePvd [NPROC] [stem] [timestep] myplot.pvd \n\n \t So, for the files listed above, to produce a pvd file that \n \t contains data for timestep 00011 from a computation with \n \t four processors the command\n\n \t \t makePvd 4 solid_soln_ 00011 solid_soln.pvd \n\n \t would create the file solid_soln.pvd which can be displayed with paraview. \n \n\v" usage() { echo -e $usagestr exit 1 } #-------------------------------------------------------- # Function to extract the step number from a filename, # assuming that the step is the number immediately # in front of the dot, stripping out leading zeroes, so # the step number of file fluid19_soln_proc342_00222.vtu # is 222. #-------------------------------------------------------- function get_step_number { echo $1 | awk 'BEGIN {found_dot=0} { number="" # look at each character, starting at end for(i=length($0);i>=1;i--) { # get the character to be checked char=substr($0,i,1) # Havent found the dot yet; keep looking if (found_dot==0) { if (char==".") { found_dot=1 } } # Have passed the dot; now read out all numbers and collect them # Bail out once we find the first letter. else { # Is the next character a number? if (match(char,"[0-9]")) { # If so, append it to record of number number=char number } else { # Else weve reached a letter so bail out break } } } # Now look at each character in number, starting at front, # to strip out leading zeroes output_number="" found_first_non_zero=0 for(i=1;i<=length(number);i++) { # get the character to be checked char=substr(number,i,1) # Ignore leading zeroes if (found_first_non_zero==0) { if (char!="0") { output_number=output_number char found_first_non_zero=1 } } # Once were past any leading zeroes # dump out everything else { output_number=output_number char } } if ( output_number=="") { output_number="0" } print output_number }' } # -- check for correct usage and assign variables if [ $# -eq 3 ]; then nbproc=$1 basefile=$2 pvdfile=$3 # -- create the PVD XML file echo ""> $pvdfile echo "">> $pvdfile echo "">> $pvdfile for ((jj=0;$jj<$nbproc;jj++)) do ii=1 for file in $basefile'proc'$jj'_'*.vt* do number=`get_step_number $file` echo "" >> $pvdfile ii=$(($ii+1)) done done elif [ $# -eq 2 ]; then basefile=$1 pvdfile=$2 # -- create the PVD XML file echo ""> $pvdfile echo "">> $pvdfile echo "">> $pvdfile ii=1 for file in $basefile*.vt* do number=`get_step_number $file` echo "" >> $pvdfile ii=$(($ii+1)) done # -- check for correct usage and assign variables elif [ $# -eq 4 ]; then nbproc=$1 basefile=$2 timestep=$3 pvdfile=$4 # -- create the PVD XML file echo ""> $pvdfile echo "">> $pvdfile echo "">> $pvdfile for ((jj=0;$jj<$nbproc;jj++)) do ii=1 for file in $basefile'proc'$jj'_'$timestep.vt* do number=`get_step_number $file` echo "" >> $pvdfile ii=$(($ii+1)) done done else usage fi echo "">> $pvdfile echo "">> $pvdfile echo " " echo " --> File $pvdfile created" echo " "