add optional path to gmsh/getdp

DiffractionGratings/grating3D_parallel_Mmatrix.sh

 #!/bin/bash
+
+### set threads to 1: parallelization is handled by gnuparallel (NPROC) only
 export OPENBLAS_NUM_THREADS=1
 export OMP_NUM_THREADS=1
 export NPROC=96
 
+### set gmsh/getdp path if necessary
+# export GMSHPATH='/path/to/onelabdir'
+# export GETDPPATH='/path/to/onelabdir'
+export GMSHPATH=''
+export GETDPPATH=''
+
 ### choose configuration
 ### theta loop study for the "U" case
 ### config 1
@@ -27,7 +35,7 @@ export myDir="res_Matrix_nb_lam"$nb_lam"_nb_"$flag_angle_study$nb_angle"_total"$
 
 rm -r $myDir
 mkdir $myDir
-gmsh grating3D.geo -setstring test_case $GRATING_CASE -3 -o grating3D.msh
+$GMSHPATH/gmsh grating3D.geo -setstring test_case $GRATING_CASE -3 -o grating3D.msh
 
 myfunc() {
     local mysubDir=$myDir/run_lam$1_$flag_angle_study$2_psi$3
@@ -43,7 +51,7 @@ myfunc() {
     fi
     local psi=$(echo "scale=10;90*$3" | bc )
     cd $mysubDir
-    getdp grating3D.pro -pre helmholtz_vector -msh grating3D.msh -cal -pos postop_helmholtz_vector -petsc_prealloc 200 -setstring test_case $GRATING_CASE -setnumber lambda0 $lam -setnumber thetadeg $theta -setnumber phideg $phi -setnumber psideg $psi -setnumber FLAG_TOTAL $FLAG_TOTAL
+    $GETDPPATH/getdp grating3D.pro -pre helmholtz_vector -msh grating3D.msh -cal -pos postop_helmholtz_vector -petsc_prealloc 200 -setstring test_case $GRATING_CASE -setnumber lambda0 $lam -setnumber thetadeg $theta -setnumber phideg $phi -setnumber psideg $psi -setnumber FLAG_TOTAL $FLAG_TOTAL
     if [ $3 -eq 0 ]; then cp res3D/rs.txt ../r_pin_sout_lam$1_$flag_angle_study$2.out ; fi
     if [ $3 -eq 0 ]; then cp res3D/rp.txt ../r_pin_pout_lam$1_$flag_angle_study$2.out ; fi
     if [ $3 -eq 1 ]; then cp res3D/rs.txt ../r_sin_sout_lam$1_$flag_angle_study$2.out ; fi