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commit 69ce8a1efeb6850ccf461bf81d7cccd3d64aa6ea 1 parent 2e93ff3
Xie Qingguang authored
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12 examples/USER/sph/sdpd-polymer-3D-test/addpolymer.awk
@@ -97,6 +97,8 @@ inatoms{
END {
printf("\nBonds\n\n")
ibond = 0
+ipoly=0
+printf("") > "poly.id"
for (q=1; q<iatom; q++) {
if (isbound(q)) {
ibond++
@@ -104,6 +106,14 @@ END {
jp = q+1
bondtype=1
print ibond, bondtype, ip, jp
- }
+if (ip != prev) {
+if (prev>0) {
+print prev, ipoly >> "poly.id"
+}
+ ipoly++
+ }
+ print ip, ipoly >> "poly.id"
+ prev=jp
+}
}
}
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1,003,055 examples/USER/sph/sdpd-polymer-3D-test/log.lammps
1,003,055 additions, 0 deletions not shown
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17,135 examples/USER/sph/sdpd-polymer-3D-test/poly3.txt
13,051 additions, 4,084 deletions not shown
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BIN  examples/USER/sph/sdpd-polymer-3D-test/poly3d.restart
Binary file not shown
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17,137 examples/USER/sph/sdpd-polymer-3D-test/poly3d.txt
13,052 additions, 4,085 deletions not shown
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7 examples/USER/sph/sdpd-polymer-3D-test/post.sh
@@ -1,6 +1,7 @@
#! /bin/bash
rm -rf punto.dat
-awk 'fl{print $3, $4,$5, $6, $7, $8} /ITEM: ATOMS/{fl=1}' *.dat > punto.dat
-#for filename in dump*.dat; do echo $filename; sed '1,8d' $filename > ${filename/.dat/.del};done
-#awk 'fl{print $1, $2, $3, $4} /ITEM: ATOMS/{fl=1}' *.del > punto.dat
+rm -rf pdata
+awk 'fl{print $3, $4, $5, $6,$7,$8} /ITEM: ATOMS/{fl=1}' dumpreal*.dat > punto.dat
+awk -f extpolymer.awk dumpreal*.dat
+#octave -q --eval "ext"
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788,906 examples/USER/sph/sdpd-polymer-3D-test/punto.dat
784,289 additions, 4,617 deletions not shown
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2  examples/USER/sph/sdpd-polymer-3D-test/run3d.sh
@@ -2,7 +2,7 @@
-rm -rf dum* im*
+rm -rf dum* im* poly* log.lammps
../../../../src/lmp_linux -in sdpd-polymer3D-inti.lmp
../../../../tools/restart2data poly3d.restart poly3d.txt
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2  examples/USER/sph/sdpd-polymer-3D-test/sdpd-polymer3D-inti.lmp
@@ -9,7 +9,7 @@ boundary p p p
# create simulation box
#3D box
-variable L equal 4.0e-4
+variable L equal 5.0e-4
region box block 0.0 ${L} 0.0 ${L} 0.0 ${L} units box
create_box 1 box
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16 examples/USER/sph/sdpd-polymer-3D-test/sdpd-polymer3D-run.lmp
@@ -5,7 +5,7 @@ atom_style hybrid bond meso
boundary p p p
# create simulation box
#3D box
-variable L equal 4e-4
+variable L equal 5e-4
region box block 0.0 ${L} 0.0 ${L} 0.0 ${L} units box
read_data poly3d.txt
@@ -42,18 +42,24 @@ variable etot equal c_ke+c_esph
# do full time integration for shear driver and fluid, but keep walls stationary
fix integrate_fix_full all meso
-dump dump_id all custom 100 dump*.dat id type x y z vx vy vz c_rho_peratom
+dump dump_id all custom 10000 dump*.dat id type x y z vx vy vz c_rho_peratom
+#dump the unwrapped coordinate of particles
+dump dumpreal_id all custom 10000 dumpreal*.dat id type xu yu zu vx vy vz c_rho_peratom
dump_modify dump_id first yes
dump_modify dump_id sort id
dump_modify dump_id pad 8
+dump_modify dumpreal_id first yes
+dump_modify dumpreal_id sort id
+dump_modify dumpreal_id pad 8
+
thermo_style custom step c_sdpd_kin
thermo_modify norm no
thermo 1
-dump imgDump all image 100 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 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_modify imgDump pad 9
neighbor 3.0e-6 bin
-timestep 1e-7
-run 40000
+timestep 1e-9
+run 40000000
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