Fix the example according to the convention

../../rdf-adf/data.spce

 No newline at end of file

# sample script to compare and debug GPU accelerated tip4p water

# use '-sf gpu' to enables the GPU accelerated pair style

# without it the original lj/cut/tip4p/long from module KSPACE will be used

units         real

boundary      p p p

atom_style    full

bond_style    harmonic

angle_style   harmonic

atom_modify   map array

pair_style    lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0

pair_modify   table 0

#long-range solver for TIP4P from module KSPACE works on CPU

suffix off

newton on

kspace_style  pppm/tip4p 1.0e-5

suffix on

read_data     data.spce

pair_coeff    * * 0.0 0.0

pair_coeff    1 1 0.1852 3.1589

bond_coeff    1 0.0 0.9572

angle_coeff   1 0.0 104.52

group water type 1 2

#maintain the water molecule rigid

fix           1 water shake 1.0e-4 200 0 b 1 a 1

fix           2 water nve

thermo        100

thermo_style  custom step etotal ke pe temp  evdwl ecoul elong press

thermo_modify format float "%.15g"

velocity      water create 300 123

if $(is_active(package,gpu)) &

 then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz"&

 else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"

dump_modify 11 sort id

timestep      1

run           1

LAMMPS (30 Oct 2019)

#

units         real

boundary      p p p

atom_style    full

bond_style    harmonic

angle_style   harmonic

atom_modify   map array

pair_style    lj/cut/tip4p/long 1 2 1 1 0.1546 9.0 9.0

pair_modify   table 0

#long-range solver for TIP4P from module KSPACE works on CPU

suffix off

newton on

kspace_style  pppm/tip4p 1.0e-5

suffix on

read_data     data.spce

  orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)

  1 by 1 by 1 MPI processor grid

  reading atoms ...

  4500 atoms

  scanning bonds ...

  2 = max bonds/atom

  scanning angles ...

  1 = max angles/atom

  reading bonds ...

  3000 bonds

  reading angles ...

  1500 angles

  2 = max # of 1-2 neighbors

  1 = max # of 1-3 neighbors

  1 = max # of 1-4 neighbors

  2 = max # of special neighbors

  special bonds CPU = 0.00143709 secs

  read_data CPU = 0.0185545 secs

pair_coeff    * * 0.0 0.0

pair_coeff    1 1 0.1852 3.1589

bond_coeff    1 0.0 0.9572

angle_coeff   1 0.0 104.52

group water type 1 2

4500 atoms in group water

#maintain the water molecule rigid

fix           1 water shake 1.0e-4 200 0 b 1 a 1

  0 = # of size 2 clusters

  0 = # of size 3 clusters

  0 = # of size 4 clusters

  1500 = # of frozen angles

fix           2 water nve

thermo        100

thermo_style  custom step etotal ke pe temp  evdwl ecoul elong press

thermo_modify format float "%.15g"

velocity      water create 300 123

if $(is_active(package,gpu))  then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"

if 0  then "dump 11 all custom 1 dump.force_gpu id type  x y z fx fy fz" else "dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz"

dump 11 all custom 1 dump.force_cpu id type  x y z fx fy fz

dump_modify 11 sort id

timestep      1

run           1

PPPM initialization ...

  extracting TIP4P info from pair style

  using polynomial approximation for long-range coulomb (../kspace.cpp:323)

  G vector (1/distance) = 0.342797

  grid = 36 36 36

  stencil order = 5

  estimated absolute RMS force accuracy = 0.00261362

  estimated relative force accuracy = 7.87083e-06

  using double precision KISS FFT

  3d grid and FFT values/proc = 79507 46656

Neighbor list info ...

  update every 1 steps, delay 10 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 11.3092

  ghost atom cutoff = 11.3092

  binsize = 5.6546, bins = 7 7 7

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair lj/cut/tip4p/long, perpetual

      attributes: half, newton on

      pair build: half/bin/newton

      stencil: half/bin/3d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 30.18 | 30.18 | 30.18 Mbytes

Step TotEng KinEng PotEng Temp E_vdwl E_coul E_long Press 

       0 -6581.1098053463 2681.834801985 -9262.9446073313 300 3652.16918734499 90723.8782743546 -103638.992069031 20828.2770003273 

       1 -6293.09711304554 1787.55263217222 -8080.64974521776 199.96227554909 3652.66537554581 91910.2042281151 -103643.519348879 20986.2037813061 

Loop time of 0.0943946 on 1 procs for 1 steps with 4500 atoms

Performance: 0.915 ns/day, 26.221 hours/ns, 10.594 timesteps/s

101.7% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.071838   | 0.071838   | 0.071838   |   0.0 | 76.10

Bond    | 1.974e-06  | 1.974e-06  | 1.974e-06  |   0.0 |  0.00

Kspace  | 0.012686   | 0.012686   | 0.012686   |   0.0 | 13.44

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 0.00012462 | 0.00012462 | 0.00012462 |   0.0 |  0.13

Output  | 0.0093175  | 0.0093175  | 0.0093175  |   0.0 |  9.87

Modify  | 0.00038138 | 0.00038138 | 0.00038138 |   0.0 |  0.40

Other   |            | 4.484e-05  |            |       |  0.05

Nlocal:    4500 ave 4500 max 4500 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    15219 ave 15219 max 15219 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    1.37151e+06 ave 1.37151e+06 max 1.37151e+06 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 1371514

Ave neighs/atom = 304.781

Ave special neighs/atom = 2

Neighbor list builds = 0

Dangerous builds = 0

Total wall time: 0:00:00