diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 53ac20f5d9158437315402d256fc45722b63685b..190ef3b2e0389987f331f1e32ed6c416551dfb13 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -215,8 +215,8 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
- USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SMD
- USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
+ USER-MOP USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC
+ USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
set(OTHER_PACKAGES CORESHELL QEQ)
foreach(PKG ${DEFAULT_PACKAGES})
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 381dc2e99589f5702dfd4ebf3f5ec615c2dd307b..16f867b7c063a277984756a2c901ffc4881ad516 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -84,6 +84,7 @@ as contained in the file name.
"USER-MGPT"_#PKG-USER-MGPT,
"USER-MISC"_#PKG-USER-MISC,
"USER-MOFFF"_#PKG-USER-MOFFF,
+"USER-MOP"_#PKG-USER-MOP,
"USER-MOLFILE"_#PKG-USER-MOLFILE,
"USER-NETCDF"_#PKG-USER-NETCDF,
"USER-OMP"_#PKG-USER-OMP,
@@ -1572,6 +1573,29 @@ examples/USER/mofff :ul
:line
+USER-MOP package :link(PKG-USER-MOP),h4
+
+[Contents:]
+
+This package contains two compute styles: compute mop and compute mop/profile.
+
+compute mop calculates components of the local stress tensor using the method of planes, applied on one plane.
+
+compute mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
+
+[Author:] Laurent Joly (University of Lyon 1)
+Romain Vermorel at (University of Pau and Pays de l'Adour)
+
+[Supporting info:]
+
+src/USER-MOP: filenames -> commands
+src/USER-MOP/README
+"compute mop"_compute_mop.html
+"compute mop/profile"_compute_mop.html
+examples/USER/mop :ul
+
+:line
+
USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
[Contents:]
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index 7db2fa895ceaa020552d6e05502b67bc174ca54b..731cf7ff101b6589f48d2836e83d1e7c8b346e46 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -57,6 +57,7 @@ Package, Description, Doc page, Example, Library
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
+"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style mop"_compute_mop.html, USER/mop, no
"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
diff --git a/doc/src/compute_mop.txt b/doc/src/compute_mop.txt
new file mode 100644
index 0000000000000000000000000000000000000000..732f55657a5732d5703cb0e4d9b4bba29df00b05
--- /dev/null
+++ b/doc/src/compute_mop.txt
@@ -0,0 +1,111 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute mop command :h3
+compute mop/profile command :h3
+
+
+[Syntax:]
+
+compute ID group-ID style dir args keywords ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+style = {mop} or {mop/profile}
+dir = {x} or {y} or {z} is the direction normal to the plane
+args = argument specific to the compute style
+keywords = {kin} or {conf} or {total} (one of more can be specified) :ul
+ {mop} args = pos
+ pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane
+ {mop/profile} args = origin delta
+ origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane
+ delta = value (distance units) is the distance between planes :pre
+
+compute 1 all mop x lower total
+compute 1 liquid mop z 0.0 kin conf
+fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time
+fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre
+
+compute 1 all mop/profile x lower 0.1 total
+compute 1 liquid mop/profile z 0.0 0.25 kin conf
+fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre
+
+
+[Description:]
+
+Compute {mop} and compute {mop/profile} define computations that
+calculate components of the local stress tensor using the method of
+planes "(Todd)"_#mop-todd. Specifically in compute {mop} calculates 3
+components are computed in directions {dir},{x}; {dir},{y}; and
+{dir},{z}; where {dir} is the direction normal to the plane, while
+in compute {mop/profile} the profile of the stress is computed.
+
+Contrary to methods based on histograms of atomic stress (i.e. using
+"compute stress/atom"_compute_stress_atom.html), the method of planes is
+compatible with mechanical balance in heterogeneous systems and at
+interfaces "(Todd)"_#mop-todd.
+
+The stress tensor is the sum of a kinetic term and a configurational
+term, which are given respectively by Eq. (21) and Eq. (16) in
+"(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that
+atoms have crossed the plane if their positions at times t-dt and t are
+one on either side of the plane, and uses the velocity at time t-dt/2
+given by the velocity-Verlet algorithm.
+
+Between one and three keywords can be used to indicate which
+contributions to the stress must be computed: kinetic stress (kin),
+configurational stress (conf), and/or total stress (total).
+
+NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
+
+NOTE 2: The local stress does not include any Lennard-Jones tail
+corrections to the pressure added by the "pair_modify tail
+yes"_pair_modify.html command, since those are contributions to the global system pressure.
+
+[Output info:]
+
+Compute {mop} calculates a global vector (indices starting at 1), with 3
+values for each declared keyword (in the order the keywords have been
+declared). For each keyword, the stress tensor components are ordered as
+follows: stress_dir,x, stress_dir,y, and stress_dir,z.
+
+Compute {mop/profile} instead calculates a global array, with 1 column
+giving the position of the planes where the stress tensor was computed,
+and with 3 columns of values for each declared keyword (in the order the
+keywords have been declared). For each keyword, the profiles of stress
+tensor components are ordered as follows: stress_dir,x; stress_dir,y;
+and stress_dir,z.
+
+The values are in pressure "units"_units.html.
+
+The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder.
+
+[Restrictions:]
+
+This style is part of the USER-MOP package. It is only enabled if LAMMPS
+is built with that package. See the "Build package"_Build_package.html
+doc page on for more info.
+
+The method is only implemented for 3d orthogonal simulation boxes whose
+size does not change in time, and axis-aligned planes.
+
+The method only works with two-body pair interactions, because it
+requires the class method pair->single() to be implemented. In
+particular, it does not work with more than two-body pair interactions,
+intra-molecular interactions, and long range (kspace) interactions.
+
+[Related commands:]
+
+"compute stress/atom"_compute_stress_atom.html
+
+[Default:] none
+
+:line
+
+:link(mop-todd)
+[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
+Phys. Rev. E 52, 1627 (1995).
diff --git a/doc/src/computes.txt b/doc/src/computes.txt
index 46dd30f7570f7a87d9874367f67f1d4af85a2fca..c431f1c1846ff9d94cc82bc0fc915f8a1ad77179 100644
--- a/doc/src/computes.txt
+++ b/doc/src/computes.txt
@@ -55,6 +55,7 @@ Computes :h1
compute_meso_e_atom
compute_meso_rho_atom
compute_meso_t_atom
+ compute_mop
compute_msd
compute_msd_chunk
compute_msd_nongauss
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index c296ff4039e0827464ba616081d6bb9630943056..0aa382ae39bbd79da6f2a500f1d0a48ac1c1a9e7 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -446,6 +446,7 @@ compute_ke_rigid.html
compute_meso_e_atom.html
compute_meso_rho_atom.html
compute_meso_t_atom.html
+compute_mop.html
compute_msd.html
compute_msd_chunk.html
compute_msd_nongauss.html
diff --git a/src/USER-MOP/compute_mop.example b/examples/USER/mop/in.compute_mop
old mode 100755
new mode 100644
similarity index 94%
rename from src/USER-MOP/compute_mop.example
rename to examples/USER/mop/in.compute_mop
index 8dea9aecbdc441c185b70ce0138a34b1c1ac825f..ab9552796fb03b7fec94c33355e0271d4354d17e
--- a/src/USER-MOP/compute_mop.example
+++ b/examples/USER/mop/in.compute_mop
@@ -38,12 +38,12 @@ fix_modify nvtliq temp Tliq
thermo 10000
thermo_modify flush yes temp Tliq
-dump 1 all atom 10000 dump.lammpstrj
+# dump 1 all atom 10000 dump.lammpstrj
fix fxbal all balance 1000 1.05 shift z 10 1.05
velocity liquid create $T 47298 dist gaussian rot yes
run 50000
-undump 1
+# undump 1
reset_timestep 0
compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
diff --git a/examples/USER/mop/log.31Aug18.compute_mop.g++.1 b/examples/USER/mop/log.31Aug18.compute_mop.g++.1
new file mode 100644
index 0000000000000000000000000000000000000000..98b403b444837d43c52ce85d75f989198566cd8c
--- /dev/null
+++ b/examples/USER/mop/log.31Aug18.compute_mop.g++.1
@@ -0,0 +1,186 @@
+LAMMPS (31 Aug 2018)
+variable T equal 0.8
+variable p_solid equal 0.05
+
+lattice fcc 1.0
+Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
+region box block 0.0 6.0 0.0 6.0 -2.0 12.0
+create_box 2 box
+Created orthogonal box = (0 0 -3.1748) to (9.52441 9.52441 19.0488)
+ 1 by 1 by 1 MPI processor grid
+
+mass * 1.0
+pair_style lj/cut 2.5
+pair_coeff * * 1.0 1.0
+pair_coeff 1 2 0.5 1.0
+pair_coeff 2 2 0.0 0.0
+neigh_modify delay 0
+
+region solid_bottom block INF INF INF INF -1.1 0.1
+region liquid block INF INF INF INF 1.1 8.9
+region solid_up block INF INF INF INF 9.9 11.1
+
+create_atoms 1 region liquid
+Created 1080 atoms
+ Time spent = 0.000631094 secs
+delete_atoms porosity liquid 0.26 88765
+Deleted 257 atoms, new total = 823
+group liquid region liquid
+823 atoms in group liquid
+
+create_atoms 2 region solid_bottom
+Created 216 atoms
+ Time spent = 0.000221014 secs
+group solid_bottom region solid_bottom
+216 atoms in group solid_bottom
+create_atoms 2 region solid_up
+Created 216 atoms
+ Time spent = 0.000169039 secs
+group solid_up region solid_up
+216 atoms in group solid_up
+group solid union solid_bottom solid_up
+432 atoms in group solid
+
+variable faSolid equal ${p_solid}*lx*ly/count(solid_up)
+variable faSolid equal 0.05*lx*ly/count(solid_up)
+fix piston_up solid_up aveforce NULL NULL -${faSolid}
+fix piston_up solid_up aveforce NULL NULL -0.0209986841649146
+fix freeze_up solid_up setforce 0.0 0.0 NULL
+fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0
+fix nvesol solid nve
+compute Tliq liquid temp
+fix nvtliq liquid nvt temp $T $T 0.5
+fix nvtliq liquid nvt temp 0.8 $T 0.5
+fix nvtliq liquid nvt temp 0.8 0.8 0.5
+fix_modify nvtliq temp Tliq
+WARNING: Temperature for fix modify is not for group all (../fix_nh.cpp:1404)
+
+thermo 10000
+thermo_modify flush yes temp Tliq
+WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:488)
+
+# dump 1 all atom 10000 dump.lammpstrj
+
+fix fxbal all balance 1000 1.05 shift z 10 1.05
+velocity liquid create $T 47298 dist gaussian rot yes
+velocity liquid create 0.8 47298 dist gaussian rot yes
+run 50000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 7 7 16
+ 1 neighbor lists, perpetual/occasional/extra = 1 0 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+Per MPI rank memory allocation (min/avg/max) = 3.187 | 3.187 | 3.187 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.8 -3.7188573 0 -2.9328812 -0.65673631 2016
+ 10000 0.80645968 -3.2160592 0 -2.4237366 -0.17266146 2016
+ 20000 0.85787011 -3.2087113 0 -2.3658796 0.032152534 2016
+ 30000 0.76357074 -3.1761807 0 -2.4259953 -0.034009443 2016
+ 40000 0.8116632 -3.1965608 0 -2.399126 -0.030033303 2016
+ 50000 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016
+Loop time of 40.6472 on 1 procs for 50000 steps with 1255 atoms
+
+Performance: 531401.825 tau/day, 1230.097 timesteps/s
+99.7% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 28.102 | 28.102 | 28.102 | 0.0 | 69.14
+Neigh | 9.8377 | 9.8377 | 9.8377 | 0.0 | 24.20
+Comm | 0.91642 | 0.91642 | 0.91642 | 0.0 | 2.25
+Output | 0.00024581 | 0.00024581 | 0.00024581 | 0.0 | 0.00
+Modify | 1.4027 | 1.4027 | 1.4027 | 0.0 | 3.45
+Other | | 0.3879 | | | 0.95
+
+Nlocal: 1255 ave 1255 max 1255 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2268 ave 2268 max 2268 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 40149 ave 40149 max 40149 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 40149
+Ave neighs/atom = 31.9912
+Neighbor list builds = 5714
+Dangerous builds = 0
+# undump 1
+reset_timestep 0
+
+compute bin_z liquid chunk/atom bin/1d z 0.0 0.1 units box
+
+compute liquidStress_ke liquid stress/atom NULL ke
+compute liquidStress_vir liquid stress/atom NULL virial
+fix profile_z liquid ave/chunk 10 1000 10000 bin_z density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6] ave running overwrite file profile.z
+
+compute mopz0 all mop z center kin conf
+fix mopz0t all ave/time 10 1000 10000 c_mopz0[*] file mopz0.time
+
+compute moppz liquid mop/profile z 0.0 0.1 kin conf
+fix moppzt all ave/time 100 100 10000 c_moppz[*] ave running overwrite file moppz.time mode vector
+
+run 40000
+Neighbor list info ...
+ update every 1 steps, delay 0 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 2.8
+ ghost atom cutoff = 2.8
+ binsize = 1.4, bins = 7 7 16
+ 3 neighbor lists, perpetual/occasional/extra = 1 2 0
+ (1) pair lj/cut, perpetual
+ attributes: half, newton on
+ pair build: half/bin/atomonly/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) compute mop, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+ (3) compute mop/profile, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 4.186 | 4.186 | 4.186 Mbytes
+Step Temp E_pair E_mol TotEng Press Volume
+ 0 0.83600463 -3.1878245 0 -2.3664749 0.054158845 2016
+ 10000 0.80600425 -3.1900933 0 -2.3982182 -0.042750667 2016
+ 20000 0.78117978 -3.2121798 0 -2.444694 0.0092285451 2016
+ 30000 0.81008494 -3.1728363 0 -2.376952 0.053347807 2016
+ 40000 0.80440016 -3.1768915 0 -2.3865924 -0.0075214347 2016
+Loop time of 45.4499 on 1 procs for 40000 steps with 1255 atoms
+
+Performance: 380198.462 tau/day, 880.089 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 25.456 | 25.456 | 25.456 | 0.0 | 56.01
+Neigh | 7.9422 | 7.9422 | 7.9422 | 0.0 | 17.47
+Comm | 0.73477 | 0.73477 | 0.73477 | 0.0 | 1.62
+Output | 0.00010562 | 0.00010562 | 0.00010562 | 0.0 | 0.00
+Modify | 11.004 | 11.004 | 11.004 | 0.0 | 24.21
+Other | | 0.3131 | | | 0.69
+
+Nlocal: 1255 ave 1255 max 1255 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 2269 ave 2269 max 2269 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 40325 ave 40325 max 40325 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 40325
+Ave neighs/atom = 32.1315
+Neighbor list builds = 4587
+Dangerous builds = 0
+
+Total wall time: 0:01:26
diff --git a/examples/USER/mop/moppz.time.reference b/examples/USER/mop/moppz.time.reference
new file mode 100644
index 0000000000000000000000000000000000000000..f8d4b532ea814d7627ecee5d365098dd47fbd8f0
--- /dev/null
+++ b/examples/USER/mop/moppz.time.reference
@@ -0,0 +1,226 @@
+# Time-averaged data for fix moppzt
+# TimeStep Number-of-rows
+# Row c_moppz[1] c_moppz[2] c_moppz[3] c_moppz[4] c_moppz[5] c_moppz[6] c_moppz[7]
+40000 222
+1 -3.1 0 0 0 0 0 0
+2 -3 0 0 0 0 0 0
+3 -2.9 0 0 0 0 0 0
+4 -2.8 0 0 0 0 0 0
+5 -2.7 0 0 0 0 0 0
+6 -2.6 0 0 0 0 0 0
+7 -2.5 0 0 0 0 0 0
+8 -2.4 0 0 0 0 0 0
+9 -2.3 0 0 0 0 0 0
+10 -2.2 0 0 0 0 0 0
+11 -2.1 0 0 0 0 0 0
+12 -2 0 0 0 0 0 0
+13 -1.9 0 0 0 0 0 0
+14 -1.8 0 0 0 0 0 0
+15 -1.7 0 0 0 0 0 0
+16 -1.6 0 0 0 0 0 0
+17 -1.5 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+18 -1.4 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+19 -1.3 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+20 -1.2 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+21 -1.1 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+22 -1 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+23 -0.9 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+24 -0.8 0 0 0 3.64631e-06 1.00467e-05 -0.00413092
+25 -0.7 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+26 -0.6 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+27 -0.5 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+28 -0.4 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+29 -0.3 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+30 -0.2 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+31 -0.1 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+32 0 0 0 0 2.27131e-05 -7.15899e-05 -0.291079
+33 0.1 0 0 0 -0.00643877 -0.00486842 0.0289193
+34 0.2 0 0 0 -0.00643877 -0.00486842 0.0289193
+35 0.3 0 0 0 -0.00643877 -0.00486842 0.0289193
+36 0.4 0 0 0 -0.00643877 -0.00486842 0.0289193
+37 0.5 0 0 0 -0.00643877 -0.00486842 0.0289193
+38 0.6 -0.00279194 0.0093508 0.013353 -0.00639358 -0.00380391 0.021025
+39 0.7 -0.00373537 0.0122501 0.0840939 -0.00503616 -0.0112127 -0.132562
+40 0.8 0.061158 -0.0280862 0.636594 0.00453591 -0.00214426 -0.557591
+41 0.9 -0.000266217 -0.0385723 0.969803 -0.0100643 0.00387732 -0.972644
+42 1 -0.0667633 -0.0208723 0.846848 0.0121337 -0.000646173 -0.936078
+43 1.1 -0.0479918 0.0444386 0.783228 0.0206387 -0.00229641 -0.640358
+44 1.2 0.0907347 -0.00458127 0.508479 0.0271462 -0.0136805 -0.427689
+45 1.3 0.0346947 -0.015182 0.397443 0.0162624 -0.0165167 -0.323227
+46 1.4 0.0576422 -0.00277706 0.359744 0.0291978 -0.0156949 -0.265795
+47 1.5 0.0596081 -0.00318334 0.238852 0.0157713 -0.0150214 -0.273303
+48 1.6 0.016955 0.0183139 0.459661 0.00421857 -0.0129777 -0.340127
+49 1.7 0.0697698 -0.0115622 0.431809 -0.0258679 0.00300245 -0.510533
+50 1.8 0.100399 -0.0797432 0.71209 -0.0501721 0.00810306 -0.680932
+51 1.9 0.0500614 -0.0191708 0.789407 -0.0486138 0.0173172 -0.750564
+52 2 -0.00914799 -0.0341791 0.626456 -0.0471521 0.000678372 -0.701829
+53 2.1 0.0369963 0.0256396 0.706456 -0.0509059 0.0173155 -0.620292
+54 2.2 -0.0579061 -0.0608427 0.484532 -0.0294166 0.000458726 -0.521648
+55 2.3 0.00709018 -0.0497913 0.439925 -0.0279961 -0.0102977 -0.43579
+56 2.4 -0.00695344 -0.000619047 0.441961 -0.0248115 -0.0244491 -0.417814
+57 2.5 -0.0375477 0.0725146 0.521221 -0.0140031 -0.0302539 -0.426543
+58 2.6 -0.00333415 0.0411399 0.550053 -0.0244236 -0.0246652 -0.444765
+59 2.7 0.0325652 -0.0422058 0.421026 -0.00606598 -0.038332 -0.507456
+60 2.8 -0.0246015 -0.0468897 0.635467 -0.035645 -0.0428363 -0.541653
+61 2.9 -0.00247499 0.00564888 0.643559 -0.0442198 -0.0211607 -0.539113
+62 3 -0.0320027 -0.0392749 0.603448 -0.0273872 -0.0458147 -0.544274
+63 3.1 -0.00250831 0.0294524 0.630966 -0.0228213 -0.00709569 -0.534171
+64 3.2 -0.0115271 0.0256808 0.597281 -0.00722677 0.00276478 -0.493192
+65 3.3 -0.00826942 -0.0763258 0.569383 -0.0294055 0.00152838 -0.470596
+66 3.4 -4.4607e-05 0.00409392 0.454468 0.00536302 0.00576224 -0.443972
+67 3.5 -0.00145279 -0.0180142 0.532694 0.0162497 0.0129368 -0.488614
+68 3.6 -0.0435087 -0.0436055 0.544955 0.0257295 0.0204122 -0.51687
+69 3.7 -0.0154394 0.0136176 0.609813 0.0132893 -0.00555839 -0.551156
+70 3.8 -0.011446 -0.00706375 0.661117 0.0380525 0.0191365 -0.531052
+71 3.9 -0.0804251 -0.0761665 0.563738 0.0489132 0.0190947 -0.509251
+72 4 0.0127481 0.0455454 0.566261 0.038016 0.0126592 -0.515555
+73 4.1 -0.00153026 -0.025983 0.584368 0.0243742 0.00388593 -0.487748
+74 4.2 0.0488435 0.00522856 0.535885 0.0161854 -0.000859699 -0.487082
+75 4.3 -0.118588 0.134127 0.503423 -0.00404382 -0.00428885 -0.494589
+76 4.4 0.0134608 -0.0373908 0.598776 -0.0285097 -0.00468738 -0.48047
+77 4.5 0.0765487 0.055302 0.608029 -0.0450575 -0.0157753 -0.509701
+78 4.6 -0.05585 -0.0462818 0.618931 -0.0170038 -0.0358189 -0.55692
+79 4.7 0.0164839 -0.0352014 0.611466 -0.0237058 -0.0240414 -0.617077
+80 4.8 0.0436038 -0.00458656 0.612365 0.00997088 -0.0562156 -0.613109
+81 4.9 0.0352871 -0.0611231 0.776314 0.0338943 -0.0604021 -0.613378
+82 5 -0.0568251 -0.0247083 0.510044 0.00279028 -0.028082 -0.595866
+83 5.1 -1.10188e-05 -0.0120973 0.53437 0.00398708 -0.02584 -0.573631
+84 5.2 0.00992898 0.0313027 0.59329 0.00561749 0.00711019 -0.522198
+85 5.3 0.00120683 -0.0356538 0.548184 -0.0200955 0.0381984 -0.52012
+86 5.4 0.0762501 -0.00822531 0.541107 -0.0241871 0.0330327 -0.540077
+87 5.5 0.0461718 0.0519605 0.629188 -0.0222764 0.0226954 -0.551385
+88 5.6 -0.0590515 0.0287662 0.549344 -0.0420534 0.031427 -0.540878
+89 5.7 -0.021125 -0.0231434 0.508528 -0.0342499 0.0495904 -0.52078
+90 5.8 0.00366259 0.0218644 0.572742 -0.0417272 0.0150681 -0.502333
+91 5.9 -0.0198693 -0.0259311 0.564659 -0.0309091 0.0326989 -0.512076
+92 6 0.00390271 -0.00109073 0.543964 -0.00911548 -0.00232516 -0.51614
+93 6.1 0.0628801 -0.0660743 0.587361 0.00381158 0.0024442 -0.515185
+94 6.2 0.00152013 0.0147332 0.572594 0.0229772 0.0059129 -0.507687
+95 6.3 0.026454 0.0873166 0.571276 0.0178474 0.00279111 -0.513827
+96 6.4 0.0951526 -0.0589118 0.598299 0.00448651 0.0259024 -0.53599
+97 6.5 0.0619766 0.0863723 0.669836 -0.00873277 -0.00553461 -0.523788
+98 6.6 -0.0634325 0.0307315 0.69454 -0.0196477 0.0147324 -0.502773
+99 6.7 0.012962 0.00747902 0.51076 -0.0151695 0.0156039 -0.52839
+100 6.8 -0.039811 -0.00360989 0.6489 0.0120414 0.00259849 -0.491579
+101 6.9 -0.0327932 0.0484302 0.616791 -0.0091501 0.0040499 -0.499037
+102 7 0.0490981 0.105001 0.502159 0.0042417 0.00326159 -0.506754
+103 7.1 -0.0581682 0.0395551 0.590876 -0.00115276 0.025084 -0.510536
+104 7.2 -0.0278943 -0.0337449 0.607452 -0.0238974 0.0310696 -0.495835
+105 7.3 -0.0493484 -0.0370496 0.660977 0.0111283 0.0129981 -0.491408
+106 7.4 -0.0206342 -0.0567824 0.5974 0.0172099 -0.00710845 -0.51165
+107 7.5 -0.00940992 0.0303369 0.49934 0.0124837 -0.03568 -0.524051
+108 7.6 -0.0366305 0.0394555 0.459697 -0.00731655 -0.0233235 -0.52555
+109 7.7 -0.0110182 0.0639483 0.563437 -0.00857366 -0.00211197 -0.542335
+110 7.8 0.010323 0.0810661 0.550813 0.00585594 0.0131706 -0.540418
+111 7.9 -0.048191 0.0123444 0.551013 -0.0166757 0.00475367 -0.538792
+112 8 -0.0214946 0.0509729 0.576751 0.0195793 0.0328914 -0.532263
+113 8.1 0.0456292 0.0094789 0.558949 0.00867662 0.0158926 -0.524578
+114 8.2 -0.0512688 -0.091908 0.641645 0.00301901 0.00974779 -0.534635
+115 8.3 -0.00783193 -0.0632416 0.552394 0.00796143 0.0380808 -0.524053
+116 8.4 0.01777 -0.0376654 0.511021 0.0161297 0.0278027 -0.542342
+117 8.5 -0.0327248 -0.0899092 0.578655 0.0137482 0.0472277 -0.524035
+118 8.6 -0.0636407 -0.0252334 0.590898 -0.00601759 0.049413 -0.533022
+119 8.7 -0.0572488 0.0633104 0.744174 0.00670858 0.0337276 -0.548476
+120 8.8 -0.100349 0.0190862 0.738246 0.0194621 0.0386781 -0.547124
+121 8.9 0.0284238 -0.0710504 0.616557 -0.00223469 0.0256231 -0.545488
+122 9 0.0455527 0.0379271 0.549399 0.0219986 7.02084e-05 -0.554089
+123 9.1 -0.00572797 -0.0537564 0.619963 0.0151132 0.00535174 -0.541016
+124 9.2 0.0209666 0.0411495 0.526906 0.00505244 -0.0117546 -0.543559
+125 9.3 0.0350478 0.0441003 0.520438 -0.0102555 -0.0105673 -0.536683
+126 9.4 0.0546092 -0.0171837 0.598682 0.00942578 -0.0283571 -0.520765
+127 9.5 0.0180568 0.00850647 0.720246 0.0282267 -0.0412171 -0.533637
+128 9.6 0.0106648 0.0437645 0.575689 0.0151481 -0.0346536 -0.558032
+129 9.7 -0.155141 -0.00267266 0.637799 0.00208151 -0.0132553 -0.567237
+130 9.8 -0.00666603 -0.103109 0.55371 -0.00920682 0.0140328 -0.515539
+131 9.9 0.0146007 0.0526576 0.484032 -0.0113123 -0.0112639 -0.503197
+132 10 0.0146807 0.0352591 0.573481 0.015403 -0.0258601 -0.471611
+133 10.1 0.00213124 -0.036368 0.623151 0.00161826 -0.0216583 -0.471559
+134 10.2 -1.19073e-05 -0.0619808 0.588624 -0.0259091 0.00687593 -0.462229
+135 10.3 0.0570578 0.0539259 0.656283 -0.0441705 0.000600941 -0.490565
+136 10.4 -0.00888513 0.0460147 0.630823 -0.0474928 0.00205316 -0.502978
+137 10.5 0.0573266 0.0238284 0.547514 -0.0310441 0.00283003 -0.511855
+138 10.6 0.121504 0.0275327 0.615782 -0.030126 -0.0249915 -0.502326
+139 10.7 -0.0156129 -0.0437632 0.630716 0.00504067 -0.0180025 -0.545656
+140 10.8 -0.0218563 -0.0432434 0.605473 0.0104081 -0.041452 -0.579481
+141 10.9 -0.020486 0.0829505 0.610883 0.0122548 -0.0306657 -0.542298
+142 11 0.0195236 0.0729355 0.664827 0.0428504 -0.0338841 -0.517077
+143 11.1 0.0139034 0.0474138 0.664459 0.0249658 -0.0397278 -0.50611
+144 11.2 0.0179999 0.0121222 0.559603 0.0412521 -0.0516893 -0.454643
+145 11.3 0.0268913 -0.0259516 0.494548 0.0514919 -0.0324735 -0.432382
+146 11.4 0.0700355 0.00851857 0.474027 0.0146607 -0.0194147 -0.460328
+147 11.5 0.0274298 -0.0148551 0.667014 0.0264921 -0.0415723 -0.515389
+148 11.6 0.0463183 0.0187287 0.515272 -0.00909174 -0.0310966 -0.558989
+149 11.7 -0.0235634 -0.0412073 0.7427 -0.0125128 -0.0333824 -0.61481
+150 11.8 0.0321678 -0.0192894 0.644069 -0.0285241 -0.0157538 -0.581231
+151 11.9 -0.00435038 -0.0267837 0.544583 -0.0261629 -0.00830545 -0.547874
+152 12 -0.0336443 0.0295318 0.549275 -0.0400734 -0.00236707 -0.486501
+153 12.1 0.00727018 0.00541209 0.492761 -0.0257499 -0.00129429 -0.419029
+154 12.2 0.0283158 -0.0109625 0.530612 -0.00905248 0.000440108 -0.356769
+155 12.3 -0.0733773 0.0287381 0.36636 0.000887014 -0.0072063 -0.350062
+156 12.4 -0.0117385 -0.00497835 0.472524 0.010125 -0.00605897 -0.402028
+157 12.5 0.0748365 -0.0280141 0.641205 -0.00788459 -0.00190551 -0.514353
+158 12.6 -0.031287 -0.0304264 0.781403 -0.0189155 -0.02107 -0.651886
+159 12.7 -0.0453856 0.100627 0.761746 -0.0140253 -0.0328365 -0.713566
+160 12.8 -0.024117 -0.0238699 0.732155 -0.0397416 -0.0143651 -0.632622
+161 12.9 0.0464686 -0.00881426 0.518078 -0.01575 0.0039229 -0.477048
+162 13 0.0662285 -0.053418 0.494651 -0.0215236 -0.00156911 -0.31744
+163 13.1 -0.00957157 -0.0114031 0.198665 -0.0144126 -0.00116237 -0.165427
+164 13.2 0.0148721 -0.0146141 0.144808 -0.013809 0.00154277 -0.0432649
+165 13.3 0.0130082 -0.0195798 0.0662957 -0.0178279 0.00125713 0.0215737
+166 13.4 0.000829942 -0.00381453 0.00218714 -0.0108116 0.0018927 0.0425618
+167 13.5 -0.00384864 -0.005638 0.00637594 -0.00704578 0.00378489 0.0161925
+168 13.6 0 0 0 -0.00602844 0.00291108 -0.0553474
+169 13.7 0 0 0 -0.00530979 -0.00289004 -0.14481
+170 13.8 0 0 0 -0.00906266 -0.00176311 -0.200465
+171 13.9 0 0 0 0.00289955 0.000223381 -0.252608
+172 14 0 0 0 0.00277034 -0.00194448 -0.279276
+173 14.1 0 0 0 0.000240431 -0.000785394 -0.292009
+174 14.2 0 0 0 4.27688e-05 8.277e-05 -0.289271
+175 14.3 0 0 0 -3.58165e-05 5.05721e-05 -0.265846
+176 14.4 0 0 0 -2.28735e-05 3.83404e-05 -0.211496
+177 14.5 0 0 0 -1.50266e-05 1.53466e-05 -0.143001
+178 14.6 0 0 0 -1.89125e-05 2.17035e-05 -0.0975257
+179 14.7 0 0 0 -3.9367e-06 1.12808e-05 -0.0528117
+180 14.8 0 0 0 -8.97431e-06 -2.01724e-06 -0.0235133
+181 14.9 0 0 0 -8.31871e-06 -7.90657e-07 -0.00959154
+182 15 0 0 0 -4.39578e-06 1.15242e-06 -0.00663168
+183 15.1 0 0 0 -4.81121e-06 1.14868e-06 -0.00374977
+184 15.2 0 0 0 -4.6114e-06 -1.95408e-06 -0.0028924
+185 15.3 0 0 0 -4.24836e-06 -5.84343e-06 -0.00186821
+186 15.4 0 0 0 1.63908e-07 -5.33026e-06 -0.00123763
+187 15.5 0 0 0 -4.38526e-06 -4.50778e-06 -0.000652976
+188 15.6 0 0 0 -4.21332e-07 -2.92016e-07 -0.000215754
+189 15.7 0 0 0 3.72451e-08 -1.02432e-08 -5.34533e-05
+190 15.8 0 0 0 5.31804e-08 -3.83997e-07 -3.16961e-05
+191 15.9 0 0 0 0 0 0
+192 16 0 0 0 0 0 0
+193 16.1 0 0 0 0 0 0
+194 16.2 0 0 0 0 0 0
+195 16.3 0 0 0 0 0 0
+196 16.4 0 0 0 0 0 0
+197 16.5 0 0 0 0 0 0
+198 16.6 0 0 0 0 0 0
+199 16.7 0 0 0 0 0 0
+200 16.8 0 0 0 0 0 0
+201 16.9 0 0 0 0 0 0
+202 17 0 0 0 0 0 0
+203 17.1 0 0 0 0 0 0
+204 17.2 0 0 0 0 0 0
+205 17.3 0 0 0 0 0 0
+206 17.4 0 0 0 0 0 0
+207 17.5 0 0 0 0 0 0
+208 17.6 0 0 0 0 0 0
+209 17.7 0 0 0 0 0 0
+210 17.8 0 0 0 0 0 0
+211 17.9 0 0 0 0 0 0
+212 18 0 0 0 0 0 0
+213 18.1 0 0 0 0 0 0
+214 18.2 0 0 0 0 0 0
+215 18.3 0 0 0 0 0 0
+216 18.4 0 0 0 0 0 0
+217 18.5 0 0 0 0 0 0
+218 18.6 0 0 0 0 0 0
+219 18.7 0 0 0 0 0 0
+220 18.8 0 0 0 0 0 0
+221 18.9 0 0 0 0 0 0
+222 19 0 0 0 0 0 0
diff --git a/examples/USER/mop/mopz0.time.reference b/examples/USER/mop/mopz0.time.reference
new file mode 100644
index 0000000000000000000000000000000000000000..6341d2290689112e4fd3a52cfb94971267d41468
--- /dev/null
+++ b/examples/USER/mop/mopz0.time.reference
@@ -0,0 +1,6 @@
+# Time-averaged data for fix mopz0t
+# TimeStep c_mopz0[1] c_mopz0[2] c_mopz0[3] c_mopz0[4] c_mopz0[5] c_mopz0[6]
+10000 -0.0267908 -0.0366912 0.634417 0.00702203 0.00200985 -0.552264
+20000 0.0202912 -0.0217482 0.597513 -0.00157669 -0.00587006 -0.537147
+30000 -0.00244239 -0.02829 0.616384 0.00640645 0.00932437 -0.561132
+40000 0.00541112 -0.0764546 0.613812 -0.00450554 -0.0038376 -0.537305
diff --git a/examples/USER/mop/profile.z.reference b/examples/USER/mop/profile.z.reference
new file mode 100644
index 0000000000000000000000000000000000000000..1e0d1bf26b10bd0c08091cfbd89cbde7f8da2607
--- /dev/null
+++ b/examples/USER/mop/profile.z.reference
@@ -0,0 +1,227 @@
+# Chunk-averaged data for fix profile_z and group temp
+# Timestep Number-of-chunks Total-count
+# Chunk Coord1 Ncount density/number temp c_liquidStress_ke[1] c_liquidStress_ke[2] c_liquidStress_ke[3] c_liquidStress_ke[4] c_liquidStress_ke[5] c_liquidStress_ke[6] c_liquidStress_vir[1] c_liquidStress_vir[2] c_liquidStress_vir[3] c_liquidStress_vir[4] c_liquidStress_vir[5] c_liquidStress_vir[6]
+40000 223 3292
+ 1 -3.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 2 -3.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 3 -2.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 4 -2.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 5 -2.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 6 -2.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 7 -2.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 8 -2.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 9 -2.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 10 -2.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 11 -2.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 12 -2.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 13 -1.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 14 -1.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 15 -1.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 16 -1.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 17 -1.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 18 -1.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 19 -1.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 20 -1.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 21 -1.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 22 -1.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 23 -0.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 24 -0.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 25 -0.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 26 -0.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 27 -0.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 28 -0.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 29 -0.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 30 -0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 31 -0.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 32 -0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 33 0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 34 0.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 35 0.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 36 0.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 37 0.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 38 0.55 0.0155 0.00170866 0.77827 -0.823106 -0.662616 -0.84909 0.0895728 -0.0915996 -0.0170938 -9.39041 -10.0498 -10.5424 -0.265868 -0.0729269 -0.626454
+ 39 0.65 0.65625 0.0723425 0.805015 -0.786824 -0.81346 -0.814762 0.0155975 0.0168616 -0.0213122 -2.89739 -2.89092 -5.81642 -0.0313195 0.230066 -0.0388364
+ 40 0.75 4.18625 0.461476 0.79884 -0.814511 -0.792997 -0.789012 -0.00942159 0.00597072 -0.00127992 -0.0143748 -0.0512459 -2.64067 0.0488393 0.0797603 0.0243815
+ 41 0.85 9.79625 1.0799 0.79714 -0.80439 -0.79918 -0.78785 -0.00331374 0.00487411 -0.00151215 1.12418 1.08693 -0.84425 -0.00560715 -0.00540606 0.0136964
+ 42 0.95 11.8853 1.31018 0.796174 -0.794167 -0.80514 -0.789215 0.00723814 -0.00234092 0.00056184 1.42901 1.47052 0.953436 0.0152978 -0.00835816 -0.0143227
+ 43 1.05 9.50925 1.04826 0.790145 -0.778307 -0.798065 -0.794064 -0.00458567 0.00288496 0.00383306 1.34248 1.35909 2.2058 -0.00480159 -0.00651465 0.0107925
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+ 142 10.95 6.7635 0.745582 0.798061 -0.789976 -0.809984 -0.794224 0.00610151 -0.00222378 0.0067858 0.790524 0.81595 0.597829 -0.0170772 -0.0118633 -0.00667559
+ 143 11.05 6.3715 0.70237 0.812611 -0.804489 -0.818657 -0.814685 -0.0111996 0.00212941 -0.0105114 0.79318 0.694842 0.430366 0.0162314 0.0306282 -0.0432507
+ 144 11.15 5.99025 0.660342 0.810481 -0.804842 -0.802955 -0.823644 0.0136279 -0.00477508 -0.00804219 0.735454 0.788358 0.431007 -0.0429171 0.000235044 0.0207342
+ 145 11.25 5.84825 0.644689 0.800577 -0.781391 -0.800625 -0.819715 0.0131729 0.00482168 0.00221727 0.739467 0.715937 0.679698 -0.0104751 -0.0177938 0.00468151
+ 146 11.35 6.0255 0.664228 0.799503 -0.790112 -0.813938 -0.79446 0.00610092 -0.00356609 0.00528215 0.663651 0.637587 0.775373 -0.0220442 0.0110108 -0.0254637
+ 147 11.45 6.4185 0.707551 0.800508 -0.790724 -0.818412 -0.792388 -0.00176802 -0.0100995 -0.000335942 0.737901 0.721074 1.00438 0.0121646 0.00623362 0.0474194
+ 148 11.55 6.9715 0.768512 0.805139 -0.797432 -0.807462 -0.810523 -0.00796199 -0.00562452 0.0109241 0.863915 0.846335 1.03536 0.00595087 0.0354208 -0.0354538
+ 149 11.65 7.39025 0.814673 0.800299 -0.790752 -0.800359 -0.809785 0.0077273 -0.00196671 0.0143455 0.981896 0.904562 0.815978 0.0281116 -0.0101508 -0.00830514
+ 150 11.75 7.559 0.833275 0.804182 -0.797492 -0.821158 -0.793896 -0.00217041 -0.00332521 0.0148471 0.933679 0.943555 0.534203 -0.0199665 0.0151777 -0.0302653
+ 151 11.85 7.1315 0.786149 0.799652 -0.787936 -0.802805 -0.808216 -1.44908e-06 -0.00827519 0.00814354 0.921138 0.86743 0.261532 -0.0419633 0.0566948 0.00841213
+ 152 11.95 6.519 0.71863 0.78074 -0.763149 -0.783572 -0.795498 -0.00379871 -0.00342527 0.00752232 0.851756 0.804143 0.110285 0.0165043 0.00177522 0.0160939
+ 153 12.05 5.634 0.621071 0.799883 -0.783563 -0.791871 -0.824217 -0.00679318 -0.00866834 0.0052431 0.805076 0.803557 0.0383568 -0.026581 -0.0194137 0.0178838
+ 154 12.15 4.98975 0.550051 0.806936 -0.791348 -0.817952 -0.811509 -0.00921572 -0.00495598 0.00885217 0.879583 0.767305 0.334965 0.026939 0.0293647 0.000599804
+ 155 12.25 4.67 0.514803 0.799596 -0.786031 -0.813879 -0.798877 0.0147599 0.0038695 -0.000385119 0.905699 0.756996 0.706379 0.0435025 -0.0270389 -0.0105177
+ 156 12.35 4.8605 0.535803 0.792597 -0.782034 -0.800663 -0.795094 0.0103921 0.00513862 -0.000697123 0.968845 0.877114 1.3359 0.0579161 -0.00865127 0.00675404
+ 157 12.45 5.67475 0.625563 0.799256 -0.7987 -0.798169 -0.800899 0.013181 0.00498032 -0.00201841 1.05353 1.03394 1.81682 0.0679688 0.0278211 -0.0228821
+ 158 12.55 7.18325 0.791854 0.810347 -0.810077 -0.814291 -0.806672 0.00606941 0.00378615 -0.00723346 1.19284 1.19182 1.73528 -0.0195636 0.00861507 0.00981433
+ 159 12.65 8.364 0.922015 0.802831 -0.793745 -0.815213 -0.799533 0.00888945 -0.00221246 -0.0013096 1.28316 1.24633 1.27452 -0.00603367 0.0133191 0.001417
+ 160 12.75 8.39525 0.92546 0.800371 -0.787459 -0.809856 -0.803797 0.00118127 0.00299289 -0.000135661 1.19417 1.20767 0.720865 -0.0135762 0.00482602 0.00623344
+ 161 12.85 6.92675 0.763578 0.798754 -0.79668 -0.801189 -0.798394 -0.00251568 0.00367251 -0.000655615 1.05994 1.04185 0.204339 0.044213 -0.0055401 0.030704
+ 162 12.95 5.13075 0.565594 0.81208 -0.834401 -0.804813 -0.797027 0.00305957 0.00144876 -0.00793753 0.856388 0.890923 -0.41972 0.0506972 0.019741 0.00876421
+ 163 13.05 3.40875 0.375768 0.799165 -0.816098 -0.797641 -0.783757 0.00113601 -0.00364604 -0.00220459 0.675005 0.636073 -1.09022 0.0229893 0.0509697 -0.0359039
+ 164 13.15 1.8995 0.209394 0.807532 -0.785503 -0.814629 -0.822464 0.025825 -0.0395374 -0.000260578 -0.0119014 0.121821 -1.87804 -0.0788917 -0.134749 -0.067008
+ 165 13.25 0.8055 0.0887952 0.843214 -0.810206 -0.880537 -0.838901 0.039551 -0.0997588 0.0234894 -2.39237 -2.01058 -4.14878 0.223851 0.231795 -0.352153
+ 166 13.35 0.272 0.0299842 0.666721 -0.779612 -0.626689 -0.593862 -0.0393791 0.00154035 -0.00625556 -1.37505 -1.38233 -3.36414 0.00300675 -0.0372793 -0.243736
+ 167 13.45 0.07925 0.00873622 0.782435 -1.07607 -0.598123 -0.673115 0.117468 0.1185 -0.0878719 -3.7526 -3.60044 -5.09311 0.910831 0.205838 -0.276478
+ 168 13.55 0.0095 0.00104724 0.19248 -0.161758 -0.293769 -0.121913 0.0596029 -0.0388238 0.000461593 -0.419057 -0.823036 -1.04983 0.0273182 -0.129878 0.392706
+ 169 13.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 170 13.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 171 13.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 172 13.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 173 14.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 174 14.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 175 14.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 176 14.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 177 14.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 178 14.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 179 14.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 180 14.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 181 14.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 182 14.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 183 15.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 184 15.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 185 15.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 186 15.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 187 15.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 188 15.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 189 15.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 190 15.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 191 15.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 192 15.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 193 16.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 194 16.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 195 16.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 196 16.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 197 16.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 198 16.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 199 16.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 200 16.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 201 16.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 202 16.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 203 17.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 204 17.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 205 17.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 206 17.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 207 17.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 208 17.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 209 17.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 210 17.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 211 17.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 212 17.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 213 18.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 214 18.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 215 18.25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 216 18.35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 217 18.45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 218 18.55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 219 18.65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 220 18.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 221 18.85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 222 18.95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+ 223 19.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
diff --git a/src/.gitignore b/src/.gitignore
index df3a22a5cd08b1a924aadde018674d972f340a5f..c7aaa8ab644e4e8987e561d121668a387e420224 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -288,6 +288,10 @@
/compute_meso_rho_atom.h
/compute_meso_t_atom.cpp
/compute_meso_t_atom.h
+/compute_mop.cpp
+/compute_mop.h
+/compute_mop_profile.cpp
+/compute_mop_profile.h
/compute_msd_nongauss.cpp
/compute_msd_nongauss.h
/compute_pe_tally.cpp
diff --git a/src/Makefile b/src/Makefile
index 948d203cfe078a51e70ca617375e0b90b44a3257..6b1a2bdb98f54271c25ad81ee197d987da5e4009 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -60,7 +60,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
user-intel user-lb user-manifold user-meamc user-meso \
- user-mgpt user-misc user-mofff user-molfile \
+ user-mgpt user-misc user-mop user-mofff user-molfile \
user-netcdf user-omp user-phonon user-qmmm user-qtb \
user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
user-uef user-vtk
diff --git a/src/USER-MOP/compute_mop.cpp b/src/USER-MOP/compute_mop.cpp
old mode 100755
new mode 100644
index 42639d73ab95450d1df132ba1417438c35419791..ba6b458172a25e3c51e7f314a15156c518a9ce3f
--- a/src/USER-MOP/compute_mop.cpp
+++ b/src/USER-MOP/compute_mop.cpp
@@ -15,10 +15,11 @@
Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
--------------------------------------------------------------------------*/
-#include "math.h"
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+
#include "compute_mop.h"
#include "atom.h"
#include "update.h"
@@ -34,8 +35,6 @@
#include "error.h"
#include "memory.h"
-#include <iostream>
-
using namespace LAMMPS_NS;
enum{X,Y,Z};
@@ -52,30 +51,25 @@ ComputeMop::ComputeMop(LAMMPS *lmp, int narg, char **arg) :
MPI_Comm_rank(world,&me);
- //set compute mode and direction of plane(s) for pressure calculation
+ // set compute mode and direction of plane(s) for pressure calculation
- if (strcmp(arg[3],"x")==0){
+ if (strcmp(arg[3],"x")==0) {
dir = X;
- }
- else if (strcmp(arg[3],"y")==0){
+ } else if (strcmp(arg[3],"y")==0) {
dir = Y;
- }
- else if (strcmp(arg[3],"z")==0){
+ } else if (strcmp(arg[3],"z")==0) {
dir = Z;
- }
- else error->all(FLERR,"Illegal compute mop command");
+ } else error->all(FLERR,"Illegal compute mop command");
+
+ // Position of the plane
- //Position of the plane
- if (strcmp(arg[4],"lower")==0){
+ if (strcmp(arg[4],"lower")==0) {
pos = domain->boxlo[dir];
- }
- else if (strcmp(arg[4],"upper")==0){
+ } else if (strcmp(arg[4],"upper")==0) {
pos = domain->boxhi[dir];
- }
- else if (strcmp(arg[4],"center")==0){
+ } else if (strcmp(arg[4],"center")==0) {
pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]);
- }
- else pos = force->numeric(FLERR,arg[4]);
+ } else pos = force->numeric(FLERR,arg[4]);
if ( pos < (domain->boxlo[dir]+domain->prd_half[dir]) ) {
pos1 = pos + domain->prd[dir];
@@ -111,19 +105,22 @@ ComputeMop::ComputeMop(LAMMPS *lmp, int narg, char **arg) :
iarg++;
}
- //Error check
- // 3D only
- if (domain->dimension<3)
- error->all(FLERR, "Compute mop incompatible with simulation dimension");
- // orthogonal simulation box
- if (domain->triclinic != 0)
- error->all(FLERR, "Compute mop incompatible with triclinic simulation box");
- // plane inside the box
- if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
- error->all(FLERR, "Plane for compute mop is out of bounds");
+ // Error check
+ // 3D only
+
+ if (domain->dimension < 3)
+ error->all(FLERR, "Compute mop incompatible with simulation dimension");
+
+ // orthogonal simulation box
+ if (domain->triclinic != 0)
+ error->all(FLERR, "Compute mop incompatible with triclinic simulation box");
+ // plane inside the box
+ if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
+ error->all(FLERR, "Plane for compute mop is out of bounds");
// Initialize some variables
+
values_local = values_global = vector = NULL;
// this fix produces a global vector
@@ -155,54 +152,60 @@ ComputeMop::~ComputeMop()
void ComputeMop::init()
{
- //Conversion constants
+ // Conversion constants
+
nktv2p = force->nktv2p;
ftm2v = force->ftm2v;
- //Plane area
+ // Plane area
+
area = 1;
int i;
for (i=0; i<3; i++){
if (i!=dir) area = area*domain->prd[i];
}
- //Timestep Value
+ // Timestep Value
+
dt = update->dt;
-// Error check
+ // Error check
-// Compute mop requires fixed simulation box
-if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
+ // Compute mop requires fixed simulation box
+ if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
error->all(FLERR, "Compute mop requires a fixed simulation box");
-//This compute requires a pair style with pair_single method implemented
-if (force->pair == NULL)
+ // This compute requires a pair style with pair_single method implemented
+
+ if (force->pair == NULL)
error->all(FLERR,"No pair style is defined for compute mop");
-if (force->pair->single_enable == 0)
+ if (force->pair->single_enable == 0)
error->all(FLERR,"Pair style does not support compute mop");
-// Warnings
-if (me==0){
- //Compute mop only accounts for pair interactions.
- // issue a warning if any intramolecular potential or Kspace is defined.
- if (force->bond!=NULL)
+ // Warnings
+
+ if (me==0){
+
+ //Compute mop only accounts for pair interactions.
+ // issue a warning if any intramolecular potential or Kspace is defined.
+
+ if (force->bond!=NULL)
error->warning(FLERR,"compute mop does not account for bond potentials");
- if (force->angle!=NULL)
+ if (force->angle!=NULL)
error->warning(FLERR,"compute mop does not account for angle potentials");
- if (force->dihedral!=NULL)
+ if (force->dihedral!=NULL)
error->warning(FLERR,"compute mop does not account for dihedral potentials");
- if (force->improper!=NULL)
+ if (force->improper!=NULL)
error->warning(FLERR,"compute mop does not account for improper potentials");
- if (force->kspace!=NULL)
- error->warning(FLERR,"compute mop does not account for kspace contributions");
- }
+ if (force->kspace!=NULL)
+ error->warning(FLERR,"compute mop does not account for kspace contributions");
+ }
// need an occasional half neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
-
}
/* ---------------------------------------------------------------------- */
@@ -219,7 +222,6 @@ void ComputeMop::init_list(int id, NeighList *ptr)
void ComputeMop::compute_vector()
{
-
invoked_array = update->ntimestep;
//Compute pressures on separate procs
@@ -259,9 +261,11 @@ void ComputeMop::compute_pairs()
// zero out arrays for one sample
+
for (i = 0; i < nvalues; i++) values_local[i] = 0.0;
// invoke half neighbor list (will copy or build if necessary)
+
neighbor->build_one(list);
inum = list->inum;
@@ -274,7 +278,8 @@ void ComputeMop::compute_pairs()
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
- //Parse values
+ // Parse values
+
double xi[3];
double vi[3];
double fi[3];
@@ -354,20 +359,13 @@ void ComputeMop::compute_pairs()
}
- if (which[m] == KIN || which[m] == TOTAL){
- //Compute kinetic contribution to pressure
- // counts local particles transfers across the plane
+ // Compute kinetic contribution to pressure
+ // counts local particles transfers across the plane
+ if (which[m] == KIN || which[m] == TOTAL){
double vcm[3];
double masstotal,sgn;
- //Velocity of the center of mass
- //int ivcm,vcmbit;
- //ivcm = igroup;
- //vcmbit = groupbit;
- //masstotal = group->mass(ivcm);
- //group->vcm(ivcm,masstotal,vcm);
-
for (int i = 0; i < nlocal; i++){
// skip if I is not in group
@@ -395,8 +393,10 @@ void ComputeMop::compute_pairs()
xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
- //because LAMMPS does not put atoms back in the box at each timestep, must check
- //atoms going through the image of the plane that is closest to the box
+ // because LAMMPS does not put atoms back in the box
+ // at each timestep, must check atoms going through the
+ // image of the plane that is closest to the box
+
double pos_temp = pos+copysign(1,domain->prd_half[dir]-pos)*domain->prd[dir];
if (fabs(xi[dir]-pos)<fabs(xi[dir]-pos_temp)) pos_temp = pos;
diff --git a/src/USER-MOP/compute_mop.h b/src/USER-MOP/compute_mop.h
old mode 100755
new mode 100644
diff --git a/src/USER-MOP/compute_mop.txt b/src/USER-MOP/compute_mop.txt
deleted file mode 100755
index ff6e85dff76714279caf7e2905229d6fd1805fb8..0000000000000000000000000000000000000000
--- a/src/USER-MOP/compute_mop.txt
+++ /dev/null
@@ -1,71 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-compute mop command :h3
-
-[Syntax:]
-
-compute ID group-ID mop dir pos keyword ... :pre
-
-ID, group-ID are documented in "compute"_compute.html command
-mop = style name of this compute command
-dir = {x} or {y} or {z} is the direction normal to the plane
-pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane
-between one and three keywords can be appended
-keyword = {kin} or {conf} or {total} :ul
-
-[Examples:]
-:link(mop-examples)
-
-compute 1 all mop x lower total
-compute 1 liquid mop z 0.0 kin conf
-fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time
-fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre
-
-[Description:]
-
-Define a computation that calculates components of the local stress tensor using the method of planes "(Todd)"_#mop-todd.
-Specifically 3 components are computed in directions {dir},{x}; {dir},{y}; and {dir},{z}; where {dir} is the direction normal to the plane.
-
-Contrary to methods based on histograms of atomic stress (i.e. using "compute stress/atom"_compute_stress_atom.html), the method of planes is compatible with mechanical balance in heterogeneous systems and at interfaces "(Todd)"_#mop-todd.
-
-The stress tensor is the sum of a kinetic term and a configurational term, which are given respectively by Eq. (21) and Eq. (16) in "(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that atoms have crossed the plane if their positions at times t-dt and t are one on either side of the plane, and uses the velocity at time t-dt/2 given by the velocity-Verlet algorithm.
-
-Between one and three keywords can be used to indicate which contributions to the stress must be computed: kinetic stress (kin), configurational stress (conf), and/or total stress (total).
-
-NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
-
-NOTE 2: The local stress does not include any Lennard-Jones tail
-corrections to the pressure added by the "pair_modify tail
-yes"_pair_modify.html command, since those are contributions to the global system pressure.
-
-[Output info:]
-
-This compute calculates a global vector (indices starting at 1), with 3 values for each declared keyword (in the order the keywords have been declared). For each keyword, the stress tensor components are ordered as follows: stress_dir,x, stress_dir,y, and stress_dir,z.
-
-The values are in pressure "units"_units.html.
-
-The values produced by this compute can be accessed by various "output commands"_Section_howto.html#howto_15. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command, see "Examples"_#mop-examples above.
-
-[Restrictions:]
-
-The method is only implemented for 3d orthogonal simulation boxes whose size does not change in time, and axis-aligned planes.
-
-The method only works with two-body pair interactions, because it requires the class method pair->single() to be implemented. In particular, it does not work with more than two-body pair interactions, intra-molecular interactions, and long range (kspace) interactions.
-
-[Related commands:]
-
-"compute mop/profile"_compute_mop_profile.html, "compute stress/atom"_compute_stress_atom.html
-
-[Default:] none
-
-:line
-
-:link(mop-todd)
-[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
-Phys. Rev. E 52, 1627 (1995).
diff --git a/src/USER-MOP/compute_mop_profile.cpp b/src/USER-MOP/compute_mop_profile.cpp
old mode 100755
new mode 100644
index 8c9e9041c418f5d45c0038cc4df8d6ac969abdfd..df62518c53f54323a63fc940b2cd8c7429bbb250
--- a/src/USER-MOP/compute_mop_profile.cpp
+++ b/src/USER-MOP/compute_mop_profile.cpp
@@ -15,10 +15,11 @@
Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
--------------------------------------------------------------------------*/
-#include "math.h"
-#include "mpi.h"
-#include "string.h"
-#include "stdlib.h"
+#include <mpi.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>
+
#include "compute_mop_profile.h"
#include "atom.h"
#include "update.h"
@@ -34,8 +35,6 @@
#include "error.h"
#include "memory.h"
-#include <iostream>
-
using namespace LAMMPS_NS;
enum{X,Y,Z};
@@ -53,20 +52,18 @@ ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) :
MPI_Comm_rank(world,&me);
- //set compute mode and direction of plane(s) for pressure calculation
+ // set compute mode and direction of plane(s) for pressure calculation
- if (strcmp(arg[3],"x")==0){
+ if (strcmp(arg[3],"x")==0) {
dir = X;
- }
- else if (strcmp(arg[3],"y")==0){
+ } else if (strcmp(arg[3],"y")==0) {
dir = Y;
- }
- else if (strcmp(arg[3],"z")==0){
+ } else if (strcmp(arg[3],"z")==0) {
dir = Z;
- }
- else error->all(FLERR,"Illegal compute mop/profile command");
+ } else error->all(FLERR,"Illegal compute mop/profile command");
+
+ // bin parameters
- //Bin parameters
if (strcmp(arg[4],"lower") == 0) originflag = LOWER;
else if (strcmp(arg[4],"center") == 0) originflag = CENTER;
else if (strcmp(arg[4],"upper") == 0) originflag = UPPER;
@@ -104,20 +101,26 @@ ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) :
iarg++;
}
- //Check domain relared errors
- // 3D only
- if (domain->dimension<3)
- error->all(FLERR, "Compute mop/profile incompatible with simulation dimension");
- // orthogonal simulation box
- if (domain->triclinic != 0)
- error->all(FLERR, "Compute mop/profile incompatible with triclinic simulation box");
+ // check domain related errors
+
+ // 3D only
+
+ if (domain->dimension < 3)
+ error->all(FLERR, "Compute mop/profile incompatible with simulation dimension");
+
+ // orthogonal simulation box
+
+ if (domain->triclinic != 0)
+ error->all(FLERR, "Compute mop/profile incompatible with triclinic simulation box");
+
+ // initialize some variables
- // Initialize some variables
nbins = 0;
coord = coordp = NULL;
values_local = values_global = array = NULL;
- //Bin setup
+ // bin setup
+
setup_bins();
// this fix produces a global array
@@ -128,7 +131,6 @@ ComputeMopProfile::ComputeMopProfile(LAMMPS *lmp, int narg, char **arg) :
array_flag = 1;
extarray = 0;
-
}
/* ---------------------------------------------------------------------- */
@@ -150,46 +152,54 @@ ComputeMopProfile::~ComputeMopProfile()
void ComputeMopProfile::init()
{
- //Conversion constants
+ // conversion constants
+
nktv2p = force->nktv2p;
ftm2v = force->ftm2v;
- //Plane area
+ // plane area
+
area = 1;
int i;
- for (i=0; i<3; i++){
+ for (i=0; i<3; i++) {
if (i!=dir) area = area*domain->prd[i];
}
- //Timestep Value
+ // timestep Value
+
dt = update->dt;
// Error check
- // Compute mop/profile requires fixed simulation box
- if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
- error->all(FLERR, "Compute mop/profile requires a fixed simulation box");
+ // Compute mop/profile requires fixed simulation box
+
+ if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
+ error->all(FLERR, "Compute mop/profile requires a fixed simulation box");
- //This compute requires a pair style with pair_single method implemented
- if (force->pair == NULL)
- error->all(FLERR,"No pair style is defined for compute mop/profile");
- if (force->pair->single_enable == 0)
- error->all(FLERR,"Pair style does not support compute mop/profile");
+ //This compute requires a pair style with pair_single method implemented
+
+ if (force->pair == NULL)
+ error->all(FLERR,"No pair style is defined for compute mop/profile");
+ if (force->pair->single_enable == 0)
+ error->all(FLERR,"Pair style does not support compute mop/profile");
- // Warnings
- if (me==0){
- //Compute mop/profile only accounts for pair interactions.
- // issue a warning if any intramolecular potential or Kspace is defined.
- if (force->bond!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for bond potentials");
- if (force->angle!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for angle potentials");
- if (force->dihedral!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for dihedral potentials");
- if (force->improper!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for improper potentials");
- if (force->kspace!=NULL)
- error->warning(FLERR,"compute mop/profile does not account for kspace contributions");
- }
+ // Warnings
+
+ if (me==0){
+
+ //Compute mop/profile only accounts for pair interactions.
+ // issue a warning if any intramolecular potential or Kspace is defined.
+
+ if (force->bond!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for bond potentials");
+ if (force->angle!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for angle potentials");
+ if (force->dihedral!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for dihedral potentials");
+ if (force->improper!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for improper potentials");
+ if (force->kspace!=NULL)
+ error->warning(FLERR,"compute mop/profile does not account for kspace contributions");
+ }
// need an occasional half neighbor list
@@ -197,7 +207,6 @@ void ComputeMopProfile::init()
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
-
}
/* ---------------------------------------------------------------------- */
@@ -214,7 +223,6 @@ void ComputeMopProfile::init_list(int id, NeighList *ptr)
void ComputeMopProfile::compute_array()
{
-
invoked_array = update->ntimestep;
//Compute pressures on separate procs
@@ -235,7 +243,6 @@ void ComputeMopProfile::compute_array()
m++;
}
}
-
}
@@ -267,6 +274,7 @@ void ComputeMopProfile::compute_pairs()
}
// invoke half neighbor list (will copy or build if necessary)
+
neighbor->build_one(list);
inum = list->inum;
@@ -279,7 +287,8 @@ void ComputeMopProfile::compute_pairs()
Pair *pair = force->pair;
double **cutsq = force->pair->cutsq;
- //Parse values
+ // parse values
+
double xi[3];
double vi[3];
double fi[3];
@@ -289,7 +298,8 @@ void ComputeMopProfile::compute_pairs()
while (m<nvalues) {
if (which[m] == CONF || which[m] == TOTAL) {
- //Compute configurational contribution to pressure
+ // Compute configurational contribution to pressure
+
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@@ -307,6 +317,7 @@ void ComputeMopProfile::compute_pairs()
j &= NEIGHMASK;
// skip if neither I nor J are in group
+
if (!(mask[i] & groupbit || mask[j] & groupbit)) continue;
xj[0] = atom->x[j][0];
@@ -326,15 +337,18 @@ void ComputeMopProfile::compute_pairs()
pos1 = coordp[ibin][0];
//check if ij pair is accross plane, add contribution to pressure
- if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ if ( ((xi[dir]>pos) && (xj[dir]<pos))
+ || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
values_local[ibin][m] += fpair*(xi[0]-xj[0])/area*nktv2p;
values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
- }
- else if ( ((xi[dir]<pos) && (xj[dir]>pos)) || ((xi[dir]<pos1) && (xj[dir]>pos1)) ){
+
+ } else if ( ((xi[dir]<pos) && (xj[dir]>pos))
+ || ((xi[dir]<pos1) && (xj[dir]>pos1)) ) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
@@ -342,9 +356,7 @@ void ComputeMopProfile::compute_pairs()
values_local[ibin][m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[ibin][m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
}
-
}
-
} else {
for (ibin=0;ibin<nbins;ibin++) {
@@ -352,7 +364,9 @@ void ComputeMopProfile::compute_pairs()
pos1 = coordp[ibin][0];
//check if ij pair is accross plane, add contribution to pressure
- if ( ((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
+
+ if ( ((xi[dir]>pos) && (xj[dir]<pos))
+ || ((xi[dir]>pos1) && (xj[dir]<pos1)) ) {
pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
@@ -360,21 +374,16 @@ void ComputeMopProfile::compute_pairs()
values_local[ibin][m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
values_local[ibin][m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
}
-
}
-
}
-
}
-
}
-
}
+ // compute kinetic contribution to pressure
+ // counts local particles transfers across the plane
if (which[m] == KIN || which[m] == TOTAL){
- //Compute kinetic contribution to pressure
- // counts local particles transfers across the plane
double vcm[3];
double masstotal,sgn;
@@ -382,6 +391,7 @@ void ComputeMopProfile::compute_pairs()
for (int i = 0; i < nlocal; i++){
// skip if I is not in group
+
if (mask[i] & groupbit){
itype = type[i];
@@ -424,9 +434,7 @@ void ComputeMopProfile::compute_pairs()
values_local[ibin][m+1] += mass[itype]*vcross[1]*sgn/dt/area*nktv2p/ftm2v;
values_local[ibin][m+2] += mass[itype]*vcross[2]*sgn/dt/area*nktv2p/ftm2v;
}
-
}
-
}
}
}
@@ -434,7 +442,6 @@ void ComputeMopProfile::compute_pairs()
}
}
-
/* ----------------------------------------------------------------------
setup 1d bins and their extent and coordinates
called at init()
@@ -486,5 +493,4 @@ void ComputeMopProfile::setup_bins()
coordp[i][0] = coord[i][0] - domain->prd[dir];
}
}
-
}
diff --git a/src/USER-MOP/compute_mop_profile.h b/src/USER-MOP/compute_mop_profile.h
old mode 100755
new mode 100644
diff --git a/src/USER-MOP/compute_mop_profile.txt b/src/USER-MOP/compute_mop_profile.txt
deleted file mode 100755
index 24b624a144e106aadeaab0e73d37471903a4b238..0000000000000000000000000000000000000000
--- a/src/USER-MOP/compute_mop_profile.txt
+++ /dev/null
@@ -1,72 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-compute mop/profile command :h3
-
-[Syntax:]
-
-compute ID group-ID mop/profile dir origin delta keyword ... :pre
-
-ID, group-ID are documented in "compute"_compute.html command
-mop/profile = style name of this compute command
-dir = {x} or {y} or {z} is the direction normal to the planes
-origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane
-delta = value (distance units) is the distance between planes
-between one and three keywords can be appended
-keyword = {kin} or {conf} or {total} :ul
-
-[Examples:]
-:link(mop-examples)
-
-compute 1 all mop/profile x lower 0.1 total
-compute 1 liquid mop/profile z 0.0 0.25 kin conf
-fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre
-
-
-[Description:]
-
-Define a computation that calculates profiles of components of the local stress tensor using the method of planes "(Todd)"_#mop-todd, applied on an array of regularly spaced planes.
-Specifically 3 components are computed in directions {dir},{x}; {dir},{y}; and {dir},{z}; where {dir} is the direction normal to the planes.
-
-Contrary to methods based on histograms of atomic stress (i.e. using "compute stress/atom"_compute_stress_atom.html), the method of planes is compatible with mechanical balance in heterogeneous systems and at interfaces "(Todd)"_#mop-todd.
-
-The stress tensor is the sum of a kinetic term and a configurational term, which are given respectively by Eq. (21) and Eq. (16) in "(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that atoms have crossed the plane if their positions at times t-dt and t are one on either side of the plane, and uses the velocity at time t-dt/2 given by the velocity-Verlet algorithm.
-
-Between one and three keywords can be used to indicate which contributions to the stress must be computed: kinetic stress (kin), configurational stress (conf), and/or total stress (total).
-
-NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
-
-NOTE 2: The local stress does not include any Lennard-Jones tail
-corrections to the pressure added by the "pair_modify tail
-yes"_pair_modify.html command, since those are contributions to the global system pressure.
-
-[Output info:]
-
-This compute calculates a global array, with 1 column giving the position of the planes where the stress tensor was computed, and with 3 columns of values for each declared keyword (in the order the keywords have been declared). For each keyword, the profiles of stress tensor components are ordered as follows: stress_dir,x; stress_dir,y; and stress_dir,z.
-
-The values are in pressure "units"_units.html.
-
-The values produced by this compute can be accessed by various "output commands"_Section_howto.html#howto_15. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command, see "Examples"_#mop-examples above.
-
-[Restrictions:]
-
-The method is only implemented for 3d orthogonal simulation boxes whose size does not change in time, and axis-aligned planes.
-
-The method only works with two-body pair interactions, because it requires the class method pair->single() to be implemented. In particular, it does not work with more than two-body pair interactions, intra-molecular interactions, and long range (kspace) interactions.
-
-[Related commands:]
-
-"compute mop"_compute_mop.html, "compute stress/atom"_compute_stress_atom.html
-
-[Default:] none
-
-:line
-
-:link(mop-todd)
-[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids",
-Phys. Rev. E 52, 1627 (1995).