Make scripts for 2D and 3D

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

@@ -0,0 +1,3 @@
+region             box block 0.0 ${Lx}  0.0 ${Ly} 0 ${Lz} units box
+create_box         1 box
+lattice            sc ${dx}

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

@@ -0,0 +1,16 @@
+variable           Ly  equal 1.803e-3
+variable           Lx  equal ${Ly}/50*20
+variable           Lz  equal ${Ly}/50*10
+variable           dx   equal 2.5e-5
+variable           sdpd_rho equal 1000
+variable           sdpd_rho0 equal 1000
+variable           sdpd_c equal 3e-2
+variable           sdpd_eta equal 1.5e-1
+variable           sdpd_background equal 0.0
+variable           sdpd_mu  equal ${sdpd_eta}/${sdpd_rho} 
+variable          h equal 2.7*${dx}
+variable          gx equal 6.12
+variable          Nfreq equal 1000
+variable          r0       equal 1.4*${dx}
+variable          H        equal 5.3e-4
+variable          sdpd_mass equal ${dx}*${dx}*${dx}*${sdpd_rho}

examples/USER/sph/sdpd-2d-polymer-fedosov/run2d.sh → examples/USER/sph/sdpd-polymer-fedosov/run.sh

@@ -10,14 +10,14 @@ else
     exit -1
 fi
 
+ndim=3d
 rm -rf dum* im* poly* log.lammps
-${lmp} -in sdpd-polymer2D-inti.lmp
+${lmp} -var ndim ${ndim} -in sdpd-polymer-init.lmp
 ${restart2data} poly3d.restart poly3d.txt
 
-
  awk -v cutoff=3.0 -v Nbeads=0 -v Nsolvent=1 -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
 
-${mpirun}  -np 2 ${lmp} -in sdpd-polymer2D-run.lmp
+${mpirun}  -np 2 ${lmp} -var ndim ${ndim} -in sdpd-polymer-run.lmp

examples/USER/sph/sdpd-2d-polymer-fedosov/sdpd-polymer2D-inti.lmp → examples/USER/sph/sdpd-polymer-fedosov/sdpd-polymer-init.lmp

@@ -1,7 +1,6 @@
 clear
 
 echo               both
-variable           ndim string  2d
 dimension          ${ndim}
 units              si
 atom_style   hybrid  bond meso
@@ -14,13 +13,7 @@ include            ${ndim}-vars.lmp
 # create fluid particles
 include            ${ndim}-lattice.lmp
 create_atoms       1 region box
-
 mass               1  ${sdpd_mass}
 
-#variable  sdpd_temp index 1.0e-5
-
-
-timestep           0.0e-5
-
 write_restart      poly3d.restart
 

examples/USER/sph/sdpd-2d-polymer-fedosov/sdpd-polymer2D-run.lmp → examples/USER/sph/sdpd-polymer-fedosov/sdpd-polymer-run.lmp

@@ -1,5 +1,4 @@
 echo               both
-variable           ndim string  2d
 dimension          ${ndim}
 units              si
 atom_style         hybrid  bond meso