Clean up mess in examples

examples/USER/sph/sdpd-3d-polymer-fedosov/run3d.sh

@@ -1,22 +1,23 @@
 #! /bin/bash
 
-
+set -e
+set -u
+configfile=$HOME/lammps-sph.sh
+if [ -f "${configfile}" ]; then
+    source "${configfile}"
+else
+    printf "cannot find config file: %s\n" ${configfile} > "/dev/stderr"
+    exit -1
+fi
 
 rm -rf dum* im* poly* log.lammps
-../../../../src/lmp_linux -in sdpd-polymer3D-inti.lmp
-../../../../tools/restart2data poly3d.restart poly3d.txt
+${lmp} -in sdpd-polymer3D-inti.lmp
+${restart2data} poly3d.restart poly3d.txt
 
 
  awk -v cutoff=3.0 -v Nbeads=25 -v Nsolvent=0 -v Npoly=full \
      -f addpolymer.awk poly3d.txt > poly3.txt
  nbound=$(tail -n 1 poly3.txt | awk '{print $1}')
  sed "s/_NUMBER_OF_BOUNDS_/$nbound/1" poly3.txt > poly3d.txt
 
-<<<<<<< HEAD
-#time /scratch/qingguang/prefix-nana/bin/mpirun -np 6  ../../../../src/lmp_linux -in sdpd-polymer3D-run.lmp
-mpiexec  -np 2 ../../../../src/lmp_linux -in sdpd-polymer3D-run.lmp
-=======
-time /scratch/qingguang/prefix-nana/bin/mpirun -np 4  ../../../../src/lmp_linux -in sdpd-polymer3D-run.lmp
-#mpirun  -np 2 ../../../../src/lmp_linux -in sdpd-polymer3D-run.lmp
->>>>>>> 5e622a9eaf08ef5c5d3c9decbc0af857c3e07727
-#../../../../src/lmp_linux -in sdpd-polymer-run.lmp
+${mpirun}  -np 2 ${lmp} -in sdpd-polymer3D-run.lmp

examples/USER/sph/sdpd-3d-polymer-fedosov/sdpd-polymer3D-run.lmp

@@ -2,8 +2,9 @@ echo               both
 variable           ndim string  3d
 dimension          ${ndim}
 units              si
-atom_style   hybrid  bond meso
-boundary          p p p
+atom_style         hybrid  bond meso
+boundary           p p p
+communicate        single vel yes
 # create simulation box
 
 #3D box
@@ -73,24 +74,15 @@ y center 0.01 v_vx_cm file vx.av ave running units reduced
 #fix av_xy_stress all ave/spatial 1 ${Nfreq} ${Nfreq} &                        
 #y lower 0.01 v_stress_pressure file sxy.av units reduced ave running      
 
-<<<<<<< HEAD
 dump               dump_id all custom 10000 dump*.dat id type x y z vx vy vz c_rho_peratom
-=======
-dump               dump_id all custom 100000 dump*.dat id type x y z vx vy vz c_rho_peratom
->>>>>>> 5e622a9eaf08ef5c5d3c9decbc0af857c3e07727
 dump_modify        dump_id first yes
 dump_modify        dump_id sort id
 dump_modify        dump_id pad 8
 
 thermo_style       custom step c_sdpd_kin
 thermo_modify      norm no
 thermo             1
-
-<<<<<<< HEAD
 dump imgDump all image 10000 image.*.jpg type type atom no bond atom 5e-6 adiam 1e-5 view 60 60 zoom 1.3  box yes 0.01
-=======
-dump imgDump all image 100000 image.*.jpg type type atom no bond atom 5e-6 adiam 1e-5 view 60 60 zoom 1.3  box yes 0.01
->>>>>>> 5e622a9eaf08ef5c5d3c9decbc0af857c3e07727
 dump_modify        imgDump pad 9