first stab at a regression test library

regtest/data/data.angle-01

@@ -0,0 +1,28 @@
+LAMMPS data file. CGCMM style. atom_style angle generated by VMD/TopoTools v1.2 on Sun Nov 20 15:31:09 EST 2011
+ 2 atoms
+ 1 bonds
+ 0 angles
+ 0 dihedrals
+ 0 impropers
+ 1 atom types
+ 1 bond types
+ 0 angle types
+ 0 dihedral types
+ 0 improper types
+  -5.0000  5.00000  xlo xhi
+  -5.0000  5.00000  ylo yhi
+ -10.0000 10.00000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1 1 0.000000 0.000000 -1.000000 # A UNK
+2 1 1 0.000000 0.000000 1.000000 # A UNK
+
+ Bonds
+
+1 1 1 2
+

regtest/data/data.angle-02

@@ -0,0 +1,37 @@
+LAMMPS data file. CGCMM style. atom_style angle generated by VMD/TopoTools v1.2 on Sun Nov 20 17:28:39 EST 2011
+ 4 atoms
+ 3 bonds
+ 2 angles
+ 0 dihedrals
+ 0 impropers
+ 1 atom types
+ 1 bond types
+ 1 angle types
+ 0 dihedral types
+ 0 improper types
+ -10.000000 10.000000  xlo xhi
+ -10.000000 10.000000  ylo yhi
+  -5.000000  5.000000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1 1 -0.750000 -0.750000 0.000000 # A UNK
+2 1 1 0.750000 -0.750000 0.000000 # A UNK
+3 1 1 -0.750000 0.750000 0.000000 # A UNK
+4 1 1 0.750000 0.750000 0.000000 # A UNK
+
+ Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+
+ Angles
+
+1 1 1 2 3
+2 1 2 3 4
+

regtest/data/data.atomic-01

@@ -0,0 +1,24 @@
+LAMMPS data file. CGCMM style. atom_style atomic generated by VMD/TopoTools v1.2 on Sun Nov 20 15:30:00 EST 2011
+ 2 atoms
+ 0 bonds
+ 0 angles
+ 0 dihedrals
+ 0 impropers
+ 1 atom types
+ 0 bond types
+ 0 angle types
+ 0 dihedral types
+ 0 improper types
+  -5.0000  5.00000  xlo xhi
+  -5.0000  5.00000  ylo yhi
+ -10.0000 10.00000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1 0.000000 0.000000 -1.000000 # A
+2 1 0.000000 0.000000 1.000000 # A
+

regtest/data/data.atomic-02

@@ -0,0 +1,26 @@
+LAMMPS data file. CGCMM style. atom_style atomic generated by VMD/TopoTools v1.2 on Sun Nov 20 17:28:13 EST 2011
+ 4 atoms
+ 0 bonds
+ 0 angles
+ 0 dihedrals
+ 0 impropers
+ 1 atom types
+ 0 bond types
+ 0 angle types
+ 0 dihedral types
+ 0 improper types
+ -10.000000 10.000000  xlo xhi
+ -10.000000 10.000000  ylo yhi
+  -5.000000  5.000000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1 -0.750000 -0.750000 0.000000 # A
+2 1 0.750000 -0.750000 0.000000 # A
+3 1 -0.750000 0.750000 0.000000 # A
+4 1 0.750000 0.750000 0.000000 # A
+

regtest/data/data.bond-01

@@ -0,0 +1,28 @@
+LAMMPS data file. CGCMM style. atom_style bond generated by VMD/TopoTools v1.2 on Sun Nov 20 15:30:59 EST 2011
+ 2 atoms
+ 1 bonds
+ 0 angles
+ 0 dihedrals
+ 0 impropers
+ 1 atom types
+ 1 bond types
+ 0 angle types
+ 0 dihedral types
+ 0 improper types
+  -5.0000  5.00000  xlo xhi
+  -5.0000  5.00000  ylo yhi
+ -10.0000 10.00000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1 1 0.000000 0.000000 -1.000000 # A UNK
+2 1 1 0.000000 0.000000 1.000000 # A UNK
+
+ Bonds
+
+1 1 1 2
+

regtest/data/data.bond-02

@@ -0,0 +1,32 @@
+LAMMPS data file. CGCMM style. atom_style bond generated by VMD/TopoTools v1.2 on Sun Nov 20 17:28:45 EST 2011
+ 4 atoms
+ 3 bonds
+ 0 angles
+ 0 dihedrals
+ 0 impropers
+ 1 atom types
+ 1 bond types
+ 0 angle types
+ 0 dihedral types
+ 0 improper types
+ -10.000000 10.000000  xlo xhi
+ -10.000000 10.000000  ylo yhi
+  -5.000000  5.000000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1 1 -0.750000 -0.750000 0.000000 # A UNK
+2 1 1 0.750000 -0.750000 0.000000 # A UNK
+3 1 1 -0.750000 0.750000 0.000000 # A UNK
+4 1 1 0.750000 0.750000 0.000000 # A UNK
+
+ Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+

regtest/data/data.charge-01

@@ -0,0 +1,24 @@
+LAMMPS data file. CGCMM style. atom_style charge generated by VMD/TopoTools v1.2 on Sun Nov 20 15:30:13 EST 2011
+ 2 atoms
+ 0 bonds
+ 0 angles
+ 0 dihedrals
+ 0 impropers
+ 1 atom types
+ 0 bond types
+ 0 angle types
+ 0 dihedral types
+ 0 improper types
+  -5.0000  5.00000  xlo xhi
+  -5.0000  5.00000  ylo yhi
+ -10.0000 10.00000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1  0.50000 0.000000 0.000000 -1.000000 # A
+2 1 -0.50000 0.000000 0.000000 1.000000 # A
+

regtest/data/data.charge-02

@@ -0,0 +1,26 @@
+LAMMPS data file. CGCMM style. atom_style charge generated by VMD/TopoTools v1.2 on Sun Nov 20 17:28:54 EST 2011
+ 4 atoms
+ 0 bonds
+ 0 angles
+ 0 dihedrals
+ 0 impropers
+ 1 atom types
+ 0 bond types
+ 0 angle types
+ 0 dihedral types
+ 0 improper types
+ -10.000000 10.000000  xlo xhi
+ -10.000000 10.000000  ylo yhi
+  -5.000000  5.000000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1 -0.333333 -0.750000 -0.750000 0.000000 # A
+2 1 -0.333333 0.750000 -0.750000 0.000000 # A
+3 1 -0.333333 -0.750000 0.750000 0.000000 # A
+4 1 1.000000 0.750000 0.750000 0.000000 # A
+

regtest/data/data.full-01

@@ -0,0 +1,28 @@
+LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.2 on Sun Nov 20 15:31:17 EST 2011
+ 2 atoms
+ 1 bonds
+ 0 angles
+ 0 dihedrals
+ 0 impropers
+ 1 atom types
+ 1 bond types
+ 0 angle types
+ 0 dihedral types
+ 0 improper types
+  -5.0000  5.00000  xlo xhi
+  -5.0000  5.00000  ylo yhi
+ -10.0000 10.00000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1 1  0.50000 0.000000 0.000000 -1.000000 # A UNK
+2 1 1 -0.50000 0.000000 0.000000 1.000000 # A UNK
+
+ Bonds
+
+1 1 1 2
+

regtest/data/data.full-02

@@ -0,0 +1,41 @@
+LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.2 on Sun Nov 20 17:28:06 EST 2011
+ 4 atoms
+ 3 bonds
+ 2 angles
+ 1 dihedrals
+ 0 impropers
+ 1 atom types
+ 1 bond types
+ 1 angle types
+ 1 dihedral types
+ 0 improper types
+ -10.000000 10.000000  xlo xhi
+ -10.000000 10.000000  ylo yhi
+  -5.000000  5.000000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1 1 -0.333333 -0.750000 -0.750000 0.000000 # A UNK
+2 1 1 -0.333333 0.750000 -0.750000 0.000000 # A UNK
+3 1 1 -0.333333 -0.750000 0.750000 0.000000 # A UNK
+4 1 1 1.000000 0.750000 0.750000 0.000000 # A UNK
+
+ Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+
+ Angles
+
+1 1 1 2 3
+2 1 2 3 4
+
+ Dihedrals
+
+1 1 1 2 3 4
+

regtest/data/data.molecular-01

@@ -0,0 +1,28 @@
+LAMMPS data file. CGCMM style. atom_style molecular generated by VMD/TopoTools v1.2 on Sun Nov 20 15:31:24 EST 2011
+ 2 atoms
+ 1 bonds
+ 0 angles
+ 0 dihedrals
+ 0 impropers
+ 1 atom types
+ 1 bond types
+ 0 angle types
+ 0 dihedral types
+ 0 improper types
+  -5.0000  5.00000  xlo xhi
+  -5.0000  5.00000  ylo yhi
+ -10.0000 10.00000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1 1 0.000000 0.000000 -1.000000 # A UNK
+2 1 1 0.000000 0.000000 1.000000 # A UNK
+
+ Bonds
+
+1 1 1 2
+

regtest/data/data.molecular-02

@@ -0,0 +1,41 @@
+LAMMPS data file. CGCMM style. atom_style molecular generated by VMD/TopoTools v1.2 on Sun Nov 20 17:27:47 EST 2011
+ 4 atoms
+ 3 bonds
+ 2 angles
+ 1 dihedrals
+ 0 impropers
+ 1 atom types
+ 1 bond types
+ 1 angle types
+ 1 dihedral types
+ 0 improper types
+ -10.000000 10.000000  xlo xhi
+ -10.000000 10.000000  ylo yhi
+  -5.000000  5.000000  zlo zhi
+
+ Masses
+
+ 1 1.000000 # A
+
+ Atoms
+
+1 1 1 -0.750000 -0.750000 0.000000 # A UNK
+2 1 1 0.750000 -0.750000 0.000000 # A UNK
+3 1 1 -0.750000 0.750000 0.000000 # A UNK
+4 1 1 0.750000 0.750000 0.000000 # A UNK
+
+ Bonds
+
+1 1 1 2
+2 1 2 3
+3 1 3 4
+
+ Angles
+
+1 1 1 2 3
+2 1 2 3 4
+
+ Dihedrals
+
+1 1 1 2 3 4
+

regtest/pair/clean.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+rm -f ref.*
+rm -f log.*

regtest/pair/common-1.inc

@@ -0,0 +1,47 @@
+
+variable newtn index on off
+label newtn
+
+variable sfx index nosfx
+variable tst index 01
+
+clear
+
+include ${sfx}.inc
+
+units lj
+atom_style ${astyle}
+special_bonds lj/coul 1.0 1.0 1.0
+special_bonds ${sbonds}
+newton ${newtn}
+
+read_data ../data/data.${astyle}-${tst}
+include ${pstyle}.inc
+
+group left  id 1
+group right id 2
+
+velocity all ramp vz -0.1 0.1 z -5.0 5.0 units box
+
+neighbor 0.3 bin
+
+fix  1 all nve
+
+compute 1 left group/group right
+
+variable force atom fx*fx+fy*fy+fz*fz
+compute 2 all pe/atom
+compute 3 all reduce sum c_2
+compute 4 left reduce sum v_force
+compute 5 right reduce sum v_force
+
+thermo 1
+thermo_style custom step etotal pe c_3 ke evdwl ecoul epair etail &
+             pxx pyy pzz pxy pxz pyz &
+             c_1[1] c_1[2] c_4 c_5 fmax fnorm
+thermo_modify format float %-16.10f
+run 10 post no
+
+next newtn
+jump SELF newtn
+

regtest/pair/compare.sh

@@ -0,0 +1,12 @@
+#!/bin/sh
+
+for s in log.* ; do \
+  t=`echo $s | sed -e 's/log./ref./'`
+  grep -v ^Loop $s | egrep -v '(OpenMP|MPI|serial)' | grep -v 'Memory usage' | sed -e 's/-0\.0000000000/0.0000000000 /g' > $t
+  if [ -f refoutput/${t}.gz ]
+  then
+     zdiff -u refoutput/${t}.gz $t && rm $t
+  else
+     echo no reference output for $s
+  fi
+done

regtest/pair/in.charged

@@ -0,0 +1,26 @@
+
+variable pstyle index lj_cut_coul_cut-01 lj_cut_coul_cut-02 lj_cut_coul_cut-03 &
+  lj_cut_coul_cut-04 lj_cut_coul_cut-05 lj_cut_coul_cut-06
+label pstyle
+
+#############################################################
+
+variable astyle index charge full
+label astyle
+
+variable sbonds index "lj/coul 1.0 1.0 1.0" "lj/coul 0.5 0.5 0.5" &
+          "lj/coul 0.0 0.0 0.0" "lj 0.0 0.0 0.0" "lj 0.5 0.5 0.5" &
+          "coul 0.0 0.0 0.0" "coul 0.5 0.5 0.5"
+label sbonds
+
+include common-1.inc
+
+next sbonds
+jump SELF sbonds
+
+next astyle
+jump SELF astyle
+
+next pstyle
+jump SELF pstyle
+

regtest/pair/in.overlay

@@ -0,0 +1,27 @@
+
+variable pstyle index lj_cut_coul_cut-overlay-01 lj_cut_coul_cut-overlay-02 &
+  lj_cut_coul_cut-overlay-03 lj_cut_coul_cut-overlay-04 &
+  lj_cut_coul_cut-overlay-05 lj_cut_coul_cut-overlay-06
+label pstyle
+
+#############################################################
+
+variable astyle index charge full
+label astyle
+
+variable sbonds index "lj/coul 1.0 1.0 1.0" "lj/coul 0.5 0.5 0.5" &
+          "lj/coul 0.0 0.0 0.0" "lj 0.0 0.0 0.0" "lj 0.5 0.5 0.5" &
+          "coul 0.0 0.0 0.0" "coul 0.5 0.5 0.5"
+label sbonds
+
+include common-1.inc
+
+next sbonds
+jump SELF sbonds
+
+next astyle
+jump SELF astyle
+
+next pstyle
+jump SELF pstyle
+

regtest/pair/in.simple

@@ -0,0 +1,25 @@
+
+variable pstyle index lj_cut-01 lj_cut-02 lj_cut-03 lj_cut-04 &
+  lj_cut-05 lj_cut-06
+label pstyle
+
+#############################################################
+
+variable astyle index atomic bond angle charge molecular full
+label astyle
+
+variable sbonds index "lj 1.0 1.0 1.0" "lj 0.5 0.5 0.5" &
+          "lj 0.0 0.0 0.0"
+label sbonds
+
+include common-1.inc
+
+next sbonds
+jump SELF sbonds
+
+next astyle
+jump SELF astyle
+
+next pstyle
+jump SELF pstyle
+

regtest/pair/lj_cut-01.inc

@@ -0,0 +1,2 @@
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0

regtest/pair/lj_cut-02.inc

@@ -0,0 +1,2 @@
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 1.9

regtest/pair/lj_cut-03.inc

@@ -0,0 +1,2 @@
+pair_style lj/cut 1.9
+pair_coeff 1 1 1.0 1.0 4.0

regtest/pair/lj_cut-04.inc

@@ -0,0 +1,3 @@
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0
+pair_modify shift yes

regtest/pair/lj_cut-05.inc

@@ -0,0 +1,3 @@
+pair_style lj/cut 2.5
+pair_coeff 1 1 1.0 1.0 1.9
+pair_modify shift yes

regtest/pair/lj_cut-06.inc

@@ -0,0 +1,3 @@
+pair_style lj/cut 1.9
+pair_coeff 1 1 1.0 1.0 4.0
+pair_modify shift yes

regtest/pair/lj_cut_coul_cut-01.inc

@@ -0,0 +1,2 @@
+pair_style lj/cut/coul/cut 2.5
+pair_coeff 1 1 1.0 1.0

regtest/pair/lj_cut_coul_cut-02.inc

@@ -0,0 +1,2 @@
+pair_style lj/cut/coul/cut 2.5 1.9
+pair_coeff 1 1 1.0 1.0 1.9

regtest/pair/lj_cut_coul_cut-03.inc

@@ -0,0 +1,2 @@
+pair_style lj/cut/coul/cut 1.9 2.5
+pair_coeff 1 1 1.0 1.0 4.0

regtest/pair/lj_cut_coul_cut-04.inc

@@ -0,0 +1,3 @@
+pair_style lj/cut/coul/cut 2.5
+pair_coeff 1 1 1.0 1.0
+pair_modify shift yes

regtest/pair/lj_cut_coul_cut-05.inc

@@ -0,0 +1,3 @@
+pair_style lj/cut/coul/cut 2.5 1.9
+pair_coeff 1 1 1.0 1.0 1.9
+pair_modify shift yes

regtest/pair/lj_cut_coul_cut-06.inc

@@ -0,0 +1,3 @@
+pair_style lj/cut/coul/cut 1.9 2.5
+pair_coeff 1 1 1.0 1.0 4.0
+pair_modify shift yes

regtest/pair/lj_cut_coul_cut-overlay-01.inc

@@ -0,0 +1,3 @@
+pair_style hybrid/overlay lj/cut 2.5 coul/cut 2.5
+pair_coeff 1 1 lj/cut 1.0 1.0
+pair_coeff 1 1 coul/cut

regtest/pair/lj_cut_coul_cut-overlay-02.inc

@@ -0,0 +1,3 @@
+pair_style hybrid/overlay lj/cut 2.5 coul/cut 1.9
+pair_coeff 1 1 lj/cut 1.0 1.0 1.9
+pair_coeff 1 1 coul/cut 1.9

regtest/pair/lj_cut_coul_cut-overlay-03.inc

@@ -0,0 +1,3 @@
+pair_style hybrid/overlay lj/cut 1.9 coul/cut 2.5
+pair_coeff 1 1 lj/cut 1.0 1.0 4.0
+pair_coeff 1 1 coul/cut 

regtest/pair/lj_cut_coul_cut-overlay-04.inc

@@ -0,0 +1,4 @@
+pair_style hybrid/overlay lj/cut 2.5 coul/cut 2.5
+pair_coeff 1 1 lj/cut 1.0 1.0
+pair_coeff 1 1 coul/cut
+pair_modify shift yes

regtest/pair/lj_cut_coul_cut-overlay-05.inc

@@ -0,0 +1,4 @@
+pair_style hybrid/overlay lj/cut 2.5 coul/cut 1.9
+pair_coeff 1 1 lj/cut 1.0 1.0 1.9
+pair_coeff 1 1 coul/cut 1.9
+pair_modify shift yes

regtest/pair/lj_cut_coul_cut-overlay-06.inc

@@ -0,0 +1,4 @@
+pair_style hybrid/overlay lj/cut 1.9 coul/cut 2.5
+pair_coeff 1 1 lj/cut 1.0 1.0 4.0
+pair_coeff 1 1 coul/cut 
+pair_modify shift yes

regtest/pair/nosfx.inc

@@ -0,0 +1,2 @@
+
+# no packages included

regtest/pair/omp-1-neigh.inc

@@ -0,0 +1,3 @@
+
+package omp 1 force/neigh
+include omp.inc

regtest/pair/omp-1-no-neigh.inc

@@ -0,0 +1,3 @@
+
+package omp 1 force
+include omp.inc

regtest/pair/omp-2-neigh.inc

@@ -0,0 +1,3 @@
+
+package omp 2 force/neigh
+include omp.inc

regtest/pair/omp-2-no-neigh.inc

@@ -0,0 +1,3 @@
+
+package omp 2 force
+include omp.inc

regtest/pair/omp-4-neigh.inc

@@ -0,0 +1,3 @@
+
+package omp 4 force/neigh
+include omp.inc

regtest/pair/omp-4-no-neigh.inc

@@ -0,0 +1,3 @@
+
+package omp 4 force
+include omp.inc

regtest/pair/omp.inc

@@ -0,0 +1,2 @@
+suffix omp
+suffix on

regtest/pair/opt.inc

@@ -0,0 +1,3 @@
+
+suffix opt
+suffix on

regtest/pair/runtests.sh

@@ -0,0 +1,40 @@
+#!/bin/sh
+
+if [ $# -lt 1 ]
+then
+   cat <<EOF
+
+  usage: $0 <command(s) to run LAMMPS>
+
+EOF
+exit 0
+fi
+
+exe="$@"
+
+export OMP_NUM_THREADS=1
+
+for tst in 01 02 ; do \
+  for sfx in nosfx opt omp-1-no-neigh omp-1-neigh omp-2-no-neigh \
+    omp-2-neigh omp-4-no-neigh omp-4-neigh ; do \
+    ${exe} -log log.simple-${tst}-${sfx} -echo none -screen none \
+           -in in.simple -var sfx ${sfx} -var tst ${tst}
+  done
+done
+
+for tst in 01 02 ; do \
+  for sfx in nosfx opt omp-1-no-neigh omp-1-neigh omp-2-no-neigh \
+    omp-2-neigh omp-4-no-neigh omp-4-neigh ; do \
+    ${exe} -log log.charged-${tst}-${sfx} -echo none -screen none \
+           -in in.charged -var sfx ${sfx} -var tst ${tst}
+  done
+done
+
+for tst in 01 02 ; do \
+  for sfx in nosfx opt omp-1-no-neigh omp-1-neigh omp-2-no-neigh \
+    omp-2-neigh omp-4-no-neigh omp-4-neigh ; do \
+    ${exe} -log log.overlay-${tst}-${sfx} -echo none -screen none \
+           -in in.overlay -var sfx ${sfx} -var tst ${tst}
+  done
+done
+

regtest/pair/updateref.sh

@@ -0,0 +1,6 @@
+#!/bin/sh
+
+for s in log.{simple,charged,overlay}* ; do \
+  t=`echo $s | sed -e 's/log./ref./'`
+  grep -v ^Loop $s | egrep -v '(OpenMP|MPI|serial)' | grep -v 'Memory usage' | sed -e 's/-0\.0000000000/0.0000000000 /g' | gzip -9 > refoutput/${t}.gz
+done