[lammps] 01/02: Update/fix autopkgtest.
Anton Gladky
gladk at moszumanska.debian.org
Sun May 18 10:22:26 UTC 2014
This is an automated email from the git hooks/post-receive script.
gladk pushed a commit to branch master
in repository lammps.
commit eff3471d298ca18cc60ea5bbd2ce579f5f9d4d71
Author: Anton Gladky <gladk at debian.org>
Date: Sun May 18 11:29:39 2014 +0200
Update/fix autopkgtest.
---
debian/tests/colloid | 71 ++++++++++++++++++
debian/tests/control | 3 +-
debian/tests/crack | 94 ++++++++++++++++++++++-
debian/tests/dipole | 61 +++++++++++++++
debian/tests/ellipse | 86 +++++++++++++++++++++
debian/tests/flow | 98 ++++++++++++++++++++++++
debian/tests/friction | 110 +++++++++++++++++++++++++++
debian/tests/hugo | 201 ++++++++++++++++++++++++++++++++++++++++++++++++++
8 files changed, 721 insertions(+), 3 deletions(-)
diff --git a/debian/tests/colloid b/debian/tests/colloid
new file mode 100755
index 0000000..cf367c5
--- /dev/null
+++ b/debian/tests/colloid
@@ -0,0 +1,71 @@
+#!/bin/sh
+# autopkgtest check
+# (C) 2014 Anton Gladky
+
+set -e
+
+export OMPI_MCA_orte_rsh_agent=/bin/false
+
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+mkdir post
+
+cat <<EOF > in.colloid
+# Big colloid particles and small LJ particles
+
+units lj
+atom_style sphere
+dimension 2
+
+lattice sq 0.01
+region box block 0 30 0 30 -0.5 0.5
+create_box 2 box
+create_atoms 1 box
+
+set group all type/fraction 2 0.96 23984
+
+set type 1 mass 9
+set type 2 mass 1
+
+velocity all create 1.44 87287 loop geom
+
+# multi neighbor and comm for efficiency
+
+neighbor 1 multi
+neigh_modify delay 0
+communicate multi
+
+# colloid potential
+
+pair_style colloid 12.5
+pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
+pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
+pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
+
+fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 &
+ mtk no pchain 0 tchain 1
+fix 2 all enforce2d
+
+#dump 1 all atom 1000 dump.colloid
+
+#dump 2 all image 1000 image.*.jpg type type &
+# zoom 1.5 center d 0.5 0.5 0.5
+#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
+
+#dump 3 all movie 1000 movie.mpg type type &
+# zoom 1.5 center d 0.5 0.5 0.5
+#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
+
+thermo_style custom step temp epair etotal press vol
+thermo 1000
+
+timestep 0.005
+
+run 50000
+
+EOF
+
+mpirun -np 2 lammps < in.colloid
+lammps < in.colloid
+echo "run: OK"
diff --git a/debian/tests/control b/debian/tests/control
index 77218b3..1fdfe6a 100644
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -1 +1,2 @@
-Tests: crack
+Tests: colloid crack dipole ellipse flow friction hugo
+Depends: lammps
diff --git a/debian/tests/crack b/debian/tests/crack
old mode 100644
new mode 100755
index d44c7c5..d5d10b6
--- a/debian/tests/crack
+++ b/debian/tests/crack
@@ -1,7 +1,97 @@
#!/bin/sh
+# autopkgtest check
+# (C) 2014 Anton Gladky
+
set -e
export OMPI_MCA_orte_rsh_agent=/bin/false
-lammps < ./examples/crack/in.crack
-mpirun -np 2 lammps < ./examples/crack/in.crack
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+mkdir post
+
+cat <<EOF > in.crack
+# 2d LJ crack simulation
+
+dimension 2
+boundary s s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.93
+region box block 0 100 0 40 -0.25 0.25
+create_box 5 box
+create_atoms 1 box
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+mass 4 1.0
+mass 5 1.0
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+region 2 block INF INF 38.75 INF INF INF
+group upper region 2
+group boundary union lower upper
+group mobile subtract all boundary
+
+region leftupper block INF 20 20 INF INF INF
+region leftlower block INF 20 INF 20 INF INF
+group leftupper region leftupper
+group leftlower region leftlower
+
+set group leftupper type 2
+set group leftlower type 3
+set group lower type 4
+set group upper type 5
+
+# initial velocities
+
+compute new mobile temp
+velocity mobile create 0.01 887723 temp new
+velocity upper set 0.0 0.3 0.0
+velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
+
+# fixes
+
+fix 1 all nve
+fix 2 boundary setforce NULL 0.0 0.0
+
+# run
+
+timestep 0.003
+thermo 200
+thermo_modify temp new
+
+neigh_modify exclude type 2 3
+
+#dump 1 all atom 500 dump.crack
+
+#dump 2 all image 250 image.*.jpg type type &
+# zoom 1.6 adiam 1.5
+#dump_modify 2 pad 4
+
+#dump 3 all movie 250 movie.mpg type type &
+# zoom 1.6 adiam 1.5
+#dump_modify 3 pad 4
+
+run 5000
+
+EOF
+
+mpirun -np 2 lammps < in.crack
+lammps < in.crack
+echo "run: OK"
diff --git a/debian/tests/dipole b/debian/tests/dipole
new file mode 100755
index 0000000..becf494
--- /dev/null
+++ b/debian/tests/dipole
@@ -0,0 +1,61 @@
+#!/bin/sh
+# autopkgtest check
+# (C) 2014 Anton Gladky
+
+set -e
+
+export OMPI_MCA_orte_rsh_agent=/bin/false
+
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+mkdir post
+
+cat <<EOF > in.dipole
+# Point dipoles in a 2d box
+
+units lj
+atom_style hybrid sphere dipole
+dimension 2
+
+lattice sq2 0.7
+region box block 0 10 0 10 -0.5 0.5
+create_box 1 box
+create_atoms 1 box
+
+# need both mass settings due to hybrid atom style
+
+mass 1 1.0
+set group all mass 1.0
+set group all dipole/random 98934 0.75
+
+velocity all create 0.0 87287 mom no
+
+pair_style lj/cut/dipole/cut 2.5
+pair_coeff * * 1.0 1.0
+
+neighbor 0.3 bin
+neigh_modify delay 0
+
+fix 1 all nve/sphere update dipole
+fix 2 all enforce2d
+
+timestep 0.005
+
+compute erot all erotate/sphere
+thermo_style custom step temp epair c_erot etotal press
+thermo 500
+
+#dump 1 all custom 500 dump.dipole id type x y z mux muy
+
+#dump 1 all image 250 image.*.jpg mux type &
+# zoom 1.6 adiam 1.2
+#dump_modify 1 pad 5
+
+run 10000
+
+EOF
+
+mpirun -np 2 lammps < in.dipole
+lammps < in.dipole
+echo "run: OK"
diff --git a/debian/tests/ellipse b/debian/tests/ellipse
new file mode 100755
index 0000000..ced2717
--- /dev/null
+++ b/debian/tests/ellipse
@@ -0,0 +1,86 @@
+#!/bin/sh
+# autopkgtest check
+# (C) 2014 Anton Gladky
+
+set -e
+
+export OMPI_MCA_orte_rsh_agent=/bin/false
+
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+mkdir post
+
+cat <<EOF > in.ellispe
+# GayBerne ellipsoids in LJ background fluid
+
+units lj
+atom_style ellipsoid
+dimension 2
+
+lattice sq 0.02
+region box block 0 20 0 20 -0.5 0.5
+create_box 2 box
+create_atoms 1 box
+
+set group all type/fraction 2 0.1 95392
+set type 1 mass 1.0
+set type 2 mass 1.5
+set type 1 shape 1 1 1
+set type 2 shape 3 1 1
+set group all quat/random 18238
+
+compute rot all temp/asphere
+group spheroid type 1
+variable dof equal count(spheroid)+2
+compute_modify rot extra \${dof}
+
+velocity all create 2.4 87287 loop geom
+
+pair_style gayberne 1.0 3.0 1.0 4.0
+pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
+pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
+pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
+
+neighbor 0.8 bin
+
+thermo_style custom step c_rot epair etotal press vol
+thermo 100
+
+timestep 0.002
+
+compute q all property/atom quatw quati quatj quatk
+
+#dump 1 all custom 100 dump.ellipse.gayberne &
+# id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
+
+#dump 2 all image 100 image.*.jpg type type &
+# zoom 1.6 center d 0.5 0.5 0.5
+#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
+
+#dump 3 all movie 100 movie.mpg type type &
+# zoom 1.6 center d 0.5 0.5 0.5
+#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
+
+fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 &
+ mtk no pchain 0 tchain 1
+fix 2 all enforce2d
+
+compute_modify 1_temp extra \${dof}
+
+# equilibrate to shrink box around dilute system
+
+run 2000
+
+# run dynamics on dense system
+
+unfix 1
+fix 1 all nve/asphere
+
+run 2000
+
+EOF
+
+mpirun -np 2 lammps < in.ellispe
+lammps < in.ellispe
+echo "run: OK"
diff --git a/debian/tests/flow b/debian/tests/flow
new file mode 100755
index 0000000..45e82af
--- /dev/null
+++ b/debian/tests/flow
@@ -0,0 +1,98 @@
+#!/bin/sh
+# autopkgtest check
+# (C) 2014 Anton Gladky
+
+set -e
+
+export OMPI_MCA_orte_rsh_agent=/bin/false
+
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+mkdir post
+
+cat <<EOF > in.flow
+# 2-d LJ flow simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.7
+region box block 0 20 0 10 -0.25 0.25
+create_box 3 box
+create_atoms 1 box
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+
+# LJ potentials
+
+pair_style lj/cut 1.12246
+pair_coeff * * 1.0 1.0 1.12246
+
+# define groups
+
+region 1 block INF INF INF 1.25 INF INF
+group lower region 1
+region 2 block INF INF 8.75 INF INF INF
+group upper region 2
+group boundary union lower upper
+group flow subtract all boundary
+
+set group lower type 2
+set group upper type 3
+
+# initial velocities
+
+compute mobile flow temp
+velocity flow create 1.0 482748 temp mobile
+fix 1 all nve
+fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
+fix_modify 2 temp mobile
+
+# Couette flow
+
+velocity lower set 0.0 0.0 0.0
+velocity upper set 3.0 0.0 0.0
+fix 3 boundary setforce 0.0 0.0 0.0
+fix 4 all enforce2d
+
+# Poiseuille flow
+
+#velocity boundary set 0.0 0.0 0.0
+#fix 3 lower setforce 0.0 0.0 0.0
+#fix 4 upper setforce 0.0 NULL 0.0
+#fix 5 upper aveforce 0.0 -1.0 0.0
+#fix 6 flow addforce 0.5 0.0 0.0
+#fix 7 all enforce2d
+
+# Run
+
+timestep 0.003
+thermo 500
+thermo_modify temp mobile
+
+#dump 1 all atom 500 dump.flow
+
+#dump 2 all image 100 image.*.jpg type type &
+# zoom 1.6 adiam 1.2
+#dump_modify 2 pad 5
+
+#dump 3 all movie 100 movie.mpg type type &
+# zoom 1.6 adiam 1.2
+#dump_modify 3 pad 5
+
+run 10000
+
+EOF
+
+mpirun -np 2 lammps < in.flow
+lammps < in.flow
+echo "run: OK"
diff --git a/debian/tests/friction b/debian/tests/friction
new file mode 100755
index 0000000..540d1c2
--- /dev/null
+++ b/debian/tests/friction
@@ -0,0 +1,110 @@
+#!/bin/sh
+# autopkgtest check
+# (C) 2014 Anton Gladky
+
+set -e
+
+export OMPI_MCA_orte_rsh_agent=/bin/false
+
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+mkdir post
+
+cat <<EOF > in.friction
+# 2d friction simulation
+
+dimension 2
+boundary p s p
+
+atom_style atomic
+neighbor 0.3 bin
+neigh_modify delay 5
+
+# create geometry
+
+lattice hex 0.9
+region box block 0 50 0 22 -0.25 0.25
+create_box 4 box
+
+mass 1 1.0
+mass 2 1.0
+mass 3 1.0
+mass 4 1.0
+
+# atom regions
+
+region lo-fixed block INF INF INF 1.1 INF INF
+region lo-slab block INF INF INF 7 INF INF
+region above-lo block INF INF INF 7 INF INF side out
+region hi-fixed block INF INF 20.9 INF INF INF
+region hi-slab block INF INF 15 INF INF INF
+region below-hi block INF INF 15 INF INF INF side out
+region lo-asperity sphere 32 7 0 8
+region hi-asperity sphere 18 15 0 8
+region lo-half-sphere intersect 2 lo-asperity above-lo
+region hi-half-sphere intersect 2 hi-asperity below-hi
+
+# create 2 surfaces with asperities
+
+create_atoms 1 region lo-slab
+create_atoms 1 region hi-slab
+create_atoms 2 region lo-half-sphere
+create_atoms 3 region hi-half-sphere
+
+# LJ potentials
+
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0 2.5
+
+# define groups
+
+group lo region lo-slab
+group lo type 2
+group hi region hi-slab
+group hi type 3
+group lo-fixed region lo-fixed
+group hi-fixed region hi-fixed
+group boundary union lo-fixed hi-fixed
+group mobile subtract all boundary
+
+set group lo-fixed type 4
+set group hi-fixed type 4
+
+# initial velocities
+
+compute new mobile temp/partial 0 1 0
+velocity mobile create 0.1 482748 temp new
+velocity hi set 1.0 0.0 0.0 sum yes
+
+# fixes
+
+fix 1 all nve
+fix 2 boundary setforce 0.0 0.0 0.0
+fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
+fix_modify 3 temp new
+fix 4 all enforce2d
+
+# Run
+
+timestep 0.0025
+thermo 1000
+thermo_modify temp new
+
+#dump 1 all atom 500 dump.friction
+
+#dump 2 all image 500 image.*.jpg type type &
+# zoom 1.6 adiam 1.5
+#dump_modify 2 pad 5
+
+#dump 3 all movie 500 movie.mpg type type &
+# zoom 1.6 adiam 1.5
+#dump_modify 3 pad 5
+
+run 20000
+
+EOF
+
+mpirun -np 2 lammps < in.friction
+lammps < in.friction
+echo "run: OK"
diff --git a/debian/tests/hugo b/debian/tests/hugo
new file mode 100755
index 0000000..76f4eb6
--- /dev/null
+++ b/debian/tests/hugo
@@ -0,0 +1,201 @@
+#!/bin/sh
+# autopkgtest check
+# (C) 2014 Anton Gladky
+
+set -e
+
+export OMPI_MCA_orte_rsh_agent=/bin/false
+
+WORKDIR=$(mktemp -d)
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+mkdir post
+
+cat <<EOF > in.hugo
+# This script reproduces stress trajectories from Fig. 1 in
+# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
+#
+# Three thermostatting scenarios are visited: undamped (nodrag),
+# damped (drag) and Nose-Hoover chain (nhchains).
+#
+# The axial and shear stress trajectories are printed to the
+# file "stress_vs_t.dat". For the damped case, the original figure
+# seems to be a plot of 2*tau, rather than tau.
+#
+# The script also demonstrates how to
+# orient a crystal along <110>,
+# and how to use the lj/cubic pair style.
+
+units lj
+boundary p p p
+
+atom_style atomic
+
+# Set up FCC lattice with z axis along <110>
+
+lattice fcc 1.4142136 &
+ orient x 0 0 1 &
+ orient y 1 -1 0 &
+ orient z 1 1 0
+
+region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
+create_box 1 mycell
+mass * 1.0
+create_atoms 1 box
+
+# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
+
+pair_style lj/cubic
+pair_coeff * * 1.0 0.8908987
+
+# Relax box dimensions
+
+fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
+
+thermo 100
+thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
+
+min_modify line quadratic
+minimize 0.0 1.0e-6 10000 100000
+
+# Define initial velocity
+
+velocity all create 0.01 87287 mom yes rot yes dist gaussian
+write_restart restart.equil
+
+# Start Run #1
+
+log log.nodrag
+
+clear
+read_restart restart.equil
+
+neighbor 0.2 bin
+neigh_modify every 1 delay 0 check yes
+timestep 0.001
+reset_timestep 0
+
+# Pzz = 40.0, drag/damping term off
+
+fix myhug all nphug temp 1.0 1.0 10.0 z 40.0 40.0 70.0 drag 0.0 tchain 1 pchain 0
+
+# Specify reference state from paper, times 1000 atoms
+
+fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
+
+# Add fix energy to ouput etotal
+
+fix_modify myhug energy yes
+
+# Define output
+
+variable dele equal f_myhug[1] # energy delta [temperature]
+variable us equal f_myhug[2] # shock velocity [distance/time]
+variable up equal f_myhug[3] # particle velocity [distance/time]
+variable pzz equal pzz # axial stress
+variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
+variable time equal dt*step
+
+thermo 1000
+thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
+
+fix stress all print 10 "\${time} \${pzz} \${tau} " screen no append stress_vs_t.dat title '#time pzz tau (no drag)'
+
+#dump id all atom 500 dump.hugoniostat
+
+#dump 2 all image 500 image.*.jpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 2 pad 5
+
+#dump 3 all movie 500 movie.mpg type type &
+# axes yes 0.8 0.02 view 60 -30
+#dump_modify 3 pad 5
+
+run 10000
+
+# Start Run #2
+
+log log.drag
+
+clear
+read_restart restart.equil
+
+neighbor 0.2 bin
+neigh_modify every 1 delay 0 check yes
+timestep 0.001
+reset_timestep 0
+
+# Pzz = 40.0, drag/damping term on
+
+fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0 drag 200.0 tchain 1 pchain 0
+
+# Specify reference state from paper, times 1000 atoms
+
+fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
+
+# Add fix energy to ouput etotal
+
+fix_modify myhug energy yes
+
+# Define output
+
+variable dele equal f_myhug[1] # energy delta [temperature]
+variable us equal f_myhug[2] # shock velocity [distance/time]
+variable up equal f_myhug[3] # particle velocity [distance/time]
+variable pzz equal pzz # axial stress
+variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
+variable time equal dt*step
+
+thermo 1000
+thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
+
+fix stress all print 10 "\${time} \${pzz} \${tau} " screen no append stress_vs_t.dat title '#time pzz tau (with drag)'
+
+run 10000
+
+# Start Run #3
+
+log log.nhchains
+
+clear
+read_restart restart.equil
+
+neighbor 0.2 bin
+neigh_modify every 1 delay 0 check yes
+timestep 0.001
+reset_timestep 0
+
+# Pzz = 40.0, drag/damping term off, Nose-Hoover chains
+
+fix myhug all nphug temp 1.0 1.0 1.0 z 40.0 40.0 70.0
+
+# Specify reference state from paper, times 1000 atoms
+
+fix_modify myhug e0 -6334.0 p0 0.0 v0 680.73519
+
+# Add fix energy to ouput etotal
+
+fix_modify myhug energy yes
+
+# Define output
+
+variable dele equal f_myhug[1] # energy delta [temperature]
+variable us equal f_myhug[2] # shock velocity [distance/time]
+variable up equal f_myhug[3] # particle velocity [distance/time]
+variable pzz equal pzz # axial stress
+variable tau equal 0.5*(pzz-0.5*(pxx+pyy)) # shear stress
+variable time equal dt*step
+
+thermo 1000
+thermo_style custom step temp ke epair etotal pzz v_tau lz f_myhug v_dele v_us v_up
+
+fix stress all print 10 "\${time} \${pzz} \${tau} " screen no append stress_vs_t.dat title '#time pzz tau (Nose-Hoover chain)'
+
+run 10000
+
+
+EOF
+
+mpirun -np 2 lammps < in.hugo
+lammps < in.hugo
+echo "run: OK"
--
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