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examples/vashishta/log.15Feb16.indiumphosphide.g++.1

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examples/vashishta/log.15Feb16.indiumphosphide.g++.4

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LAMMPS (15 Feb 2016)

# calculate the energy volume curve for InP zincblende



# define volume range and filename



variable	ndelta equal 100

variable	volatom_min equal 20.0

variable	volatom_max equal 29.0

variable	evsvolfile string evsvol.dat



# set up cell



units		metal



boundary	p p p



# setup loop variables for box volume



variable	amin equal ${volatom_min}^(1/3)*2

variable	amin equal 20^(1/3)*2

variable 	delta equal (${volatom_max}-${volatom_min})/${ndelta}

variable 	delta equal (29-${volatom_min})/${ndelta}

variable 	delta equal (29-20)/${ndelta}

variable 	delta equal (29-20)/100

variable	scale equal (${delta}/v_volatom+1)^(1/3)

variable	scale equal (0.09/v_volatom+1)^(1/3)



# set up 8 atom InP zincblende unit cell



lattice diamond ${amin}

lattice diamond 5.42883523318981

Lattice spacing in x,y,z = 5.42884 5.42884 5.42884



region		box prism 	 	0 1 		0 1 		0 1 		0 0 0



create_box	2 box

Created triclinic box = (0 0 0) to (5.42884 5.42884 5.42884) with tilt (0 0 0)

  1 by 2 by 2 MPI processor grid



create_atoms	1	box       			basis 5 2 			basis 6 2 			basis 7 2 			basis 8 2

Created 8 atoms



mass 		1 114.76

mass 		2 30.98



# choose potential



pair_style	vashishta

pair_coeff 	* * InP.vashishta In P

Reading potential file InP.vashishta with DATE: 2015-10-14



# setup neighbor style



neighbor 	1.0 nsq

neigh_modify 	once no every 1 delay 0 check yes



# setup output



thermo_style 	custom step temp pe press vol

thermo_modify 	norm no

variable 	volatom equal vol/atoms

variable 	eatom equal pe/atoms

print 		"# Volume [A^3/atom] Energy [eV/atom]" file ${evsvolfile}

print 		"# Volume [A^3/atom] Energy [eV/atom]" file evsvol.dat

# Volume [A^3/atom] Energy [eV/atom]



# loop over range of volumes



label 		loop

variable 	i loop ${ndelta}

variable 	i loop 100



change_box 	all x scale ${scale} y scale ${scale} z scale ${scale} remap

change_box 	all x scale 1.00149775560818 y scale ${scale} z scale ${scale} remap

change_box 	all x scale 1.00149775560818 y scale 1.00149775560818 z scale ${scale} remap

change_box 	all x scale 1.00149775560818 y scale 1.00149775560818 z scale 1.00149775560818 remap

  triclinic box = (-0.00406553 0 0) to (5.4329 5.42884 5.42884) with tilt (0 0 0)

  triclinic box = (-0.00406553 -0.00406553 0) to (5.4329 5.4329 5.42884) with tilt (0 0 0)

  triclinic box = (-0.00406553 -0.00406553 -0.00406553) to (5.4329 5.4329 5.4329) with tilt (0 0 0)



# calculate energy

# no energy minimization needed for zincblende



run 		0

WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 0 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 7

  ghost atom cutoff = 7

Memory usage per processor = 2.33394 Mbytes

Step Temp PotEng Press Volume 

       0            0   -24.633958     315900.5       160.72 

Loop time of 3.09944e-06 on 4 procs for 0 steps with 8 atoms



0.0% CPU use with 4 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0          | 0          | 0          |   0.0 |  0.00

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 0          | 0          | 0          |   0.0 |  0.00

Output  | 0          | 0          | 0          |   0.0 |  0.00

Modify  | 0          | 0          | 0          |   0.0 |  0.00

Other   |            | 3.099e-06  |            |       |100.00



Nlocal:    2 ave 2 max 2 min

Histogram: 4 0 0 0 0 0 0 0 0 0

Nghost:    320 ave 320 max 320 min

Histogram: 4 0 0 0 0 0 0 0 0 0

Neighs:    0 ave 0 max 0 min

Histogram: 4 0 0 0 0 0 0 0 0 0

FullNghs:  140 ave 140 max 140 min

Histogram: 4 0 0 0 0 0 0 0 0 0



Total # of neighbors = 560

Ave neighs/atom = 70

Neighbor list builds = 0

Dangerous builds = 0

print 		"${volatom} ${eatom}" append ${evsvolfile}

print 		"${volatom} ${eatom}" append evsvol.dat

20.09 -3.07924477327226



next 		i

jump 		SELF loop

ERROR: Label wasn't found in input script (../input.cpp:207)

examples/vashishta/log.15Feb16.sio2.g++.1

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LAMMPS (15 Feb 2016)

# test Vashishta potential for quartz



units		metal

boundary	p p p



atom_style	atomic



read_data	data.quartz

  triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0)

  1 by 1 by 1 MPI processor grid

  reading atoms ...

  9 atoms



replicate       4 4 4

  triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0)

  1 by 1 by 1 MPI processor grid

  576 atoms

velocity	all create 2000.0 277387 mom yes

displace_atoms	all move 0.05 0.9 0.4 units box



pair_style 	vashishta

pair_coeff	* *  SiO.1990.vashishta Si O

Reading potential file SiO.1990.vashishta with DATE: 2015-10-14



neighbor	0.3 bin

neigh_modify	delay 10



fix		1 all nve

thermo		10

timestep	0.001



#dump		1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz

#dump_modify	1 element Si O



run		100

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 10 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 10.3

  ghost atom cutoff = 10.3

  binsize = 5.15 -> bins = 6 4 5

Memory usage per processor = 2.05839 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0         2000    -5280.875            0   -5132.2259   -20502.321 

      10    895.65237    -5198.402            0    -5131.833    419.34676 

      20    932.93463   -5201.1569            0   -5131.8169   -21407.961 

      30    936.09591   -5201.3998            0   -5131.8248   -32531.168 

      40    930.05159   -5201.0073            0   -5131.8816   -46445.212 

      50    904.64676    -5199.062            0   -5131.8245   -31402.385 

      60    1005.5353   -5206.5725            0   -5131.8365   -29790.442 

      70    941.02343   -5201.7644            0   -5131.8232   -23046.796 

      80    1020.1044   -5207.6763            0   -5131.8574   -13488.675 

      90    912.75535    -5199.651            0   -5131.8108    2715.5897 

     100    998.97588   -5206.1008            0   -5131.8523    6024.3651 

Loop time of 2.1758 on 1 procs for 100 steps with 576 atoms



Performance: 3.971 ns/day, 6.044 hours/ns, 45.960 timesteps/s

99.9% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 2.096      | 2.096      | 2.096      |   0.0 | 96.33

Neigh   | 0.074266   | 0.074266   | 0.074266   |   0.0 |  3.41

Comm    | 0.0039184  | 0.0039184  | 0.0039184  |   0.0 |  0.18

Output  | 0.00011158 | 0.00011158 | 0.00011158 |   0.0 |  0.01

Modify  | 0.00092316 | 0.00092316 | 0.00092316 |   0.0 |  0.04

Other   |            | 0.0006278  |            |       |  0.03



Nlocal:    576 ave 576 max 576 min

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

Nghost:    4926 ave 4926 max 4926 min

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

Neighs:    0 ave 0 max 0 min

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

FullNghs:  210470 ave 210470 max 210470 min

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



Total # of neighbors = 210470

Ave neighs/atom = 365.399

Neighbor list builds = 10

Dangerous builds = 10



Total wall time: 0:00:02

examples/vashishta/log.15Feb16.sio2.g++.4

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LAMMPS (15 Feb 2016)

# test Vashishta potential for quartz



units		metal

boundary	p p p



atom_style	atomic



read_data	data.quartz

  triclinic box = (0 0 0) to (4.9134 4.25513 5.4052) with tilt (-2.4567 0 0)

  2 by 1 by 2 MPI processor grid

  reading atoms ...

  9 atoms



replicate       4 4 4

  triclinic box = (0 0 0) to (19.6536 17.0205 21.6208) with tilt (-9.8268 0 0)

  2 by 1 by 2 MPI processor grid

  576 atoms

velocity	all create 2000.0 277387 mom yes

displace_atoms	all move 0.05 0.9 0.4 units box



pair_style 	vashishta

pair_coeff	* *  SiO.1990.vashishta Si O

Reading potential file SiO.1990.vashishta with DATE: 2015-10-14



neighbor	0.3 bin

neigh_modify	delay 10



fix		1 all nve

thermo		10

timestep	0.001



#dump		1 all cfg 10 *.cfg mass type xs ys zs vx vy vz fx fy fz

#dump_modify	1 element Si O



run		100

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 10 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 10.3

  ghost atom cutoff = 10.3

  binsize = 5.15 -> bins = 6 4 5

Memory usage per processor = 2.00703 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0         2000    -5280.875            0   -5132.2259   -20502.321 

      10    895.65237    -5198.402            0    -5131.833    419.34676 

      20    932.93463   -5201.1569            0   -5131.8169   -21407.961 

      30    936.09591   -5201.3998            0   -5131.8248   -32531.168 

      40    930.05159   -5201.0073            0   -5131.8816   -46445.212 

      50    904.64676    -5199.062            0   -5131.8245   -31402.385 

      60    1005.5353   -5206.5725            0   -5131.8365   -29790.442 

      70    941.02343   -5201.7644            0   -5131.8232   -23046.796 

      80    1020.1044   -5207.6763            0   -5131.8574   -13488.675 

      90    912.75535    -5199.651            0   -5131.8108    2715.5897 

     100    998.97588   -5206.1008            0   -5131.8523    6024.3651 

Loop time of 0.580982 on 4 procs for 100 steps with 576 atoms



Performance: 14.871 ns/day, 1.614 hours/ns, 172.122 timesteps/s

99.7% CPU use with 4 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.51474    | 0.51703    | 0.51923    |   0.2 | 88.99

Neigh   | 0.017053   | 0.01726    | 0.017457   |   0.1 |  2.97

Comm    | 0.04357    | 0.045723   | 0.048217   |   0.8 |  7.87

Output  | 0.00022483 | 0.00024056 | 0.0002687  |   0.1 |  0.04

Modify  | 0.00026703 | 0.00027239 | 0.00027704 |   0.0 |  0.05

Other   |            | 0.0004541  |            |       |  0.08



Nlocal:    144 ave 146 max 143 min

Histogram: 2 0 0 1 0 0 0 0 0 1

Nghost:    3031 ave 3032 max 3030 min

Histogram: 1 0 0 0 0 2 0 0 0 1

Neighs:    0 ave 0 max 0 min

Histogram: 4 0 0 0 0 0 0 0 0 0

FullNghs:  52617.5 ave 53258 max 52208 min

Histogram: 2 0 0 0 1 0 0 0 0 1



Total # of neighbors = 210470

Ave neighs/atom = 365.399

Neighbor list builds = 10

Dangerous builds = 10



Total wall time: 0:00:00

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