-angle_style charmm -+
angle_style charmm
+-angle_style charmm -angle_coeff 1 300.0 107.0 50.0 3.0 -+
angle_style charmm
+angle_coeff 1 300.0 107.0 50.0 3.0
+-angle_style class2 -+
angle_style class2
+-angle_style class2 -angle_coeff * 75.0 -angle_coeff 1 bb 10.5872 1.0119 1.5228 -angle_coeff * ba 3.6551 24.895 1.0119 1.5228 -+
angle_style class2
+angle_coeff * 75.0
+angle_coeff 1 bb 10.5872 1.0119 1.5228
+angle_coeff * ba 3.6551 24.895 1.0119 1.5228
+-angle_style cosine -+
angle_style cosine
+-angle_style cosine -angle_coeff * 75.0 -+
angle_style cosine
+angle_coeff * 75.0
+-angle_style cosine/delta -+
angle_style cosine/delta
+-angle_style cosine/delta -angle_coeff 2*4 75.0 100.0 -+
angle_style cosine/delta
+angle_coeff 2*4 75.0 100.0
+-angle_style cosine/periodic -+
angle_style cosine/periodic
+-angle_style cosine/periodic -angle_coeff * 75.0 1 6 -+
angle_style cosine/periodic
+angle_coeff * 75.0 1 6
+-angle_style cosine/shift -+
angle_style cosine/shift
+-angle_style cosine/shift -angle_coeff * 10.0 45.0 -+
angle_style cosine/shift
+angle_coeff * 10.0 45.0
+-angle_style cosine/shift/exp -+
angle_style cosine/shift/exp
+-angle_style cosine/shift/exp -angle_coeff * 10.0 45.0 2.0 -+
angle_style cosine/shift/exp
+angle_coeff * 10.0 45.0 2.0
+-angle_style cosine/squared -+
angle_style cosine/squared
+-angle_style cosine/squared -angle_coeff 2*4 75.0 100.0 -+
angle_style cosine/squared
+angle_coeff 2*4 75.0 100.0
+-angle_style dipole -+
angle_style dipole
+-angle_style dipole -angle_coeff 6 2.1 180.0 -+
angle_style dipole
+angle_coeff 6 2.1 180.0
+-angle_style fourier -+
angle_style fourier
+-angle_style fourier/simple -+
angle_style fourier/simple
+-angle_style harmonic -+
angle_style harmonic
+-angle_style harmonic -angle_coeff 1 300.0 107.0 -+
angle_style harmonic
+angle_coeff 1 300.0 107.0
+-angle_style quartic -+
angle_style quartic
+-angle_style quartic -angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221 -+
angle_style quartic
+angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
+-angle_style sdk --
-angle_style sdk/omp -+
angle_style sdk
+angle_style sdk/omp
+-angle_style sdk -angle_coeff 1 300.0 107.0 -+
angle_style sdk
+angle_coeff 1 300.0 107.0
+-bond_style class2 -+
bond_style class2
+-bond_style class2 -bond_coeff 1 1.0 100.0 80.0 80.0 -+
bond_style class2
+bond_coeff 1 1.0 100.0 80.0 80.0
+-bond_style fene -+
bond_style fene
+-bond_style fene -bond_coeff 1 30.0 1.5 1.0 1.0 -+
bond_style fene
+bond_coeff 1 30.0 1.5 1.0 1.0
+-bond_style fene/expand -+
bond_style fene/expand
+-bond_style fene/expand -bond_coeff 1 30.0 1.5 1.0 1.0 0.5 -+
bond_style fene/expand
+bond_coeff 1 30.0 1.5 1.0 1.0 0.5
+-bond_style harmonic -+
bond_style harmonic
+-bond_style harmonic -bond_coeff 5 80.0 1.2 -+
bond_style harmonic
+bond_coeff 5 80.0 1.2
+-bond_style harmonic/shift -+
bond_style harmonic/shift
+-bond_style harmonic/shift -bond_coeff 5 10.0 0.5 1.0 -+
bond_style harmonic/shift
+bond_coeff 5 10.0 0.5 1.0
+-bond_style harmonic/shift/cut -+
bond_style harmonic/shift/cut
+-bond_style harmonic/shift/cut -bond_coeff 5 10.0 0.5 1.0 -+
bond_style harmonic/shift/cut
+bond_coeff 5 10.0 0.5 1.0
+-bond_style morse -+
bond_style morse
+-bond_style morse -bond_coeff 5 1.0 2.0 1.2 -+
bond_style morse
+bond_coeff 5 1.0 2.0 1.2
+-bond_style nonlinear -+
bond_style nonlinear
+-bond_style nonlinear -bond_coeff 2 100.0 1.1 1.4 -+
bond_style nonlinear
+bond_coeff 2 100.0 1.1 1.4
+-bond_style quartic -+
bond_style quartic
+-bond_style quartic -bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 -+
bond_style quartic
+bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
+Note that when bonds are dumped to a file via the dump local command, bonds with type 0 are not included. The delete_bonds command can also be used to query the status of broken bonds or permanently delete them, e.g.:
--delete_bonds all stats -delete_bonds all bond 0 remove -+
delete_bonds all stats
+delete_bonds all bond 0 remove
+Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. diff --git a/doc/html/compute_centro_atom.html b/doc/html/compute_centro_atom.html index 5b1779546e..743a69e651 100644 --- a/doc/html/compute_centro_atom.html +++ b/doc/html/compute_centro_atom.html @@ -234,7 +234,7 @@ simulation into gold (FCC). These were provided by Jon Zimmerman Free surface ~ 23.0
These values are *not* normalized by the square of the lattice +
These values are not normalized by the square of the lattice parameter. If they were, normalized values would be:
Bulk lattice = 0
Dislocation core ~ 0.06 (0.03 to 0.075)
diff --git a/doc/html/compute_fep.html b/doc/html/compute_fep.html
index 0824a98ae4..5a7910465c 100644
--- a/doc/html/compute_fep.html
+++ b/doc/html/compute_fep.html
@@ -164,10 +164,10 @@
-compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes -compute 1 all fep 300 atom charge 2 v_delta -+
compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
+compute 1 all fep 300 atom charge 2 v_delta
+The simplest way to output the results of the compute gyration/chunk calculation to a file is to use the fix ave/time command, for example:
--compute cc1 all chunk/atom molecule -compute myChunk all gyration/chunk cc1 -fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector -+
compute cc1 all chunk/atom molecule
+compute myChunk all gyration/chunk cc1
+fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+Output info:
This compute calculates a global vector if the tensor keyword is not
specified and a global array if it is. The length of the vector or
diff --git a/doc/html/compute_heat_flux.html b/doc/html/compute_heat_flux.html
index 1595174920..1ef755717d 100644
--- a/doc/html/compute_heat_flux.html
+++ b/doc/html/compute_heat_flux.html
@@ -237,30 +237,29 @@ energy/area/time # Sample LAMMPS input script for thermal conductivity of solid Ar
-units real
+units real
variable T equal 70
variable V equal vol
variable dt equal 4.0
variable p equal 200 # correlation length
variable s equal 10 # sample interval
variable d equal $p*$s # dump interval
-
+
+
# convert from LAMMPS real units to SI
-
-variable kB equal 1.3806504e-23 # [J/K] Boltzmann
+variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable kCal2J equal 4186.0/6.02214e23
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}
-
+
+
# setup problem
-
-dimension 3
+dimension 3
boundary p p p
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 4 0 4 0 4
@@ -271,7 +270,8 @@ pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405
timestep ${dt}
thermo $d
-
+
+
# equilibration and thermalization
@@ -287,8 +287,7 @@ run 8000
#fix NVE all nve
-reset_timestep 0 ++reset_timestep 0 compute myKE all ke/atom compute myPE all pe/atom compute myStress all stress/atom NULL virial @@ -306,8 +305,9 @@ thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33 run 100000 variable k equal (v_k11+v_k22+v_k33)/3.0 variable ndens equal count(all)/vol -print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3" -+print "average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3" +
-compute 1 all pressure thermo_temp -compute 1 all pressure NULL pair bond -+
compute 1 all pressure thermo_temp
+compute 1 all pressure NULL pair bond
+A compute of this style with the ID of “thermo_press” is created when LAMMPS starts up, as if this command were in the input script:
--compute thermo_press all pressure thermo_temp -+
compute thermo_press all pressure thermo_temp
+where “thermo_temp” is the ID of a similarly defined compute of style “temp”. See the “thermo_style” command for more details.
-compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5 -compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo --
-fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed -fix saed/vtk 1 1 1 c_2 file Ni_000.saed -+
compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
+compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
+fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
+fix saed/vtk 1 1 1 c_2 file Ni_000.saed
+For a mesh defined by the simulation domain, a rectilinear grid is -constructed with spacing c*inv(A) along each reciprocal lattice +constructed with spacing c*inv(A) along each reciprocal lattice axis. Where A are the vectors corresponding to the edges of the simulation cell. If one or two directions has non-periodic boundary conditions, then the spacing in these directions is defined from the diff --git a/doc/html/compute_sna_atom.html b/doc/html/compute_sna_atom.html index 930f66a12e..e61705f25a 100644 --- a/doc/html/compute_sna_atom.html +++ b/doc/html/compute_sna_atom.html @@ -134,11 +134,11 @@
-compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... -compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... -compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ... -+
compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+-for j1 in range(0,twojmax+1): - if(diagonal==2): - print j1/2.,j1/2.,j1/2. - elif(diagonal==1): - for j in range(0,min(twojmax,2*j1)+1,2): - print j1/2.,j1/2.,j/2. - elif(diagonal==0): - for j2 in range(0,j1+1): - for j in range(j1-j2,min(twojmax,j1+j2)+1,2): - print j1/2.,j2/2.,j/2. - elif(diagonal==3): - for j2 in range(0,j1+1): - for j in range(j1-j2,min(twojmax,j1+j2)+1,2): - if (j>=j1): print j1/2.,j2/2.,j/2. -+
for j1 in range(0,twojmax+1):
+ if(diagonal==2):
+ print j1/2.,j1/2.,j1/2.
+ elif(diagonal==1):
+ for j in range(0,min(twojmax,2*j1)+1,2):
+ print j1/2.,j1/2.,j/2.
+ elif(diagonal==0):
+ for j2 in range(0,j1+1):
+ for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
+ print j1/2.,j2/2.,j/2.
+ elif(diagonal==3):
+ for j2 in range(0,j1+1):
+ for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
+ if (j>=j1): print j1/2.,j2/2.,j/2.
+Compute snad/atom evaluates a per-atom array. The columns are arranged into ntypes blocks, listed in order of atom type I. Each block contains three sub-blocks corresponding to the x, y, and z diff --git a/doc/html/compute_stress_atom.html b/doc/html/compute_stress_atom.html index c4704bbbbd..e99ece1705 100644 --- a/doc/html/compute_stress_atom.html +++ b/doc/html/compute_stress_atom.html @@ -234,12 +234,12 @@ d = dimension and V is the volume of the system, the result should be -P, where P is the total pressure of the system.
These lines in an input script for a 3d system should yield that result. I.e. the last 2 columns of thermo output will be the same:
--compute peratom all stress/atom NULL -compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3] -variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol) -thermo_style custom step temp etotal press v_press -+
compute peratom all stress/atom NULL
+compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
+variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
+thermo_style custom step temp etotal press v_press
+Output info:
This compute calculates a per-atom array with 6 columns, which can be accessed by indices 1-6 by any command that uses per-atom values from diff --git a/doc/html/compute_xrd.html b/doc/html/compute_xrd.html index caeec6cf77..b16569ab91 100644 --- a/doc/html/compute_xrd.html +++ b/doc/html/compute_xrd.html @@ -159,10 +159,10 @@ compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual
-fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd -fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd -+
fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
+fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
+For a mesh defined by the simulation domain, a rectilinear grid is -constructed with spacing c*inv(A) along each reciprocal lattice +constructed with spacing c*inv(A) along each reciprocal lattice axis. Where A are the vectors corresponding to the edges of the simulation cell. If one or two directions has non-periodic boundary conditions, then the spacing in these directions is defined from the diff --git a/doc/html/create_atoms.html b/doc/html/create_atoms.html index 3786038236..03785a73f4 100644 --- a/doc/html/create_atoms.html +++ b/doc/html/create_atoms.html @@ -128,9 +128,9 @@
-create_atoms type style args keyword values ... -+
create_atoms type style args keyword values ...
+-create_atoms 1 box -create_atoms 3 region regsphere basis 2 3 -create_atoms 3 single 0 0 5 -create_atoms 1 box var v set x xpos set y ypos -+
create_atoms 1 box
+create_atoms 3 region regsphere basis 2 3
+create_atoms 3 single 0 0 5
+create_atoms 1 box var v set x xpos set y ypos
+-variable x equal 100 +++variable x equal 100 variable y equal 25 lattice hex 0.8442 region box block 0 $x 0 $y -0.5 0.5 -create_box 1 box ---variable xx equal 0.0 -variable yy equal 0.0 -variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0" -create_atoms 1 box var v set x xx set y yy -+create_box 1 box +dihedral_style charmm/omp command+variable xx equal 0.0 +variable yy equal 0.0 +variable v equal "(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) > 0.0" +create_atoms 1 box var v set x xx set y yy +Syntax
--dihedral_style charmm -++dihedral_style charmm +Examples
--dihedral_style charmm -dihedral_coeff 1 0.2 1 180 1.0 -dihedral_coeff 2 1.8 1 0 1.0 -dihedral_coeff 1 3.1 2 180 0.5 -++dihedral_style charmm +dihedral_coeff 1 0.2 1 180 1.0 +dihedral_coeff 2 1.8 1 0 1.0 +dihedral_coeff 1 3.1 2 180 0.5 +Description
diff --git a/doc/html/dihedral_class2.html b/doc/html/dihedral_class2.html index e9556733e2..40f10f1e74 100644 --- a/doc/html/dihedral_class2.html +++ b/doc/html/dihedral_class2.html @@ -131,21 +131,21 @@dihedral_style class2/omp command
Syntax
--dihedral_style class2 -++dihedral_style class2 +Examples
--dihedral_style class2 -dihedral_coeff 1 100 75 100 70 80 60 -dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 -dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010 -dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 -dihedral_coeff * aat -13.5271 110.2453 105.1270 -dihedral_coeff * bb13 0.0 1.0119 1.1010 -++dihedral_style class2 +dihedral_coeff 1 100 75 100 70 80 60 +dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 +dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010 +dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 +dihedral_coeff * aat -13.5271 110.2453 105.1270 +dihedral_coeff * bb13 0.0 1.0119 1.1010 +Description
diff --git a/doc/html/dihedral_cosine_shift_exp.html b/doc/html/dihedral_cosine_shift_exp.html index 1cc73331be..b6e718bce8 100644 --- a/doc/html/dihedral_cosine_shift_exp.html +++ b/doc/html/dihedral_cosine_shift_exp.html @@ -131,16 +131,16 @@dihedral_style cosine/shift/exp/omp command
Syntax
--dihedral_style cosine/shift/exp -++dihedral_style cosine/shift/exp +Examples
--dihedral_style cosine/shift/exp -dihedral_coeff 1 10.0 45.0 2.0 -++dihedral_style cosine/shift/exp +dihedral_coeff 1 10.0 45.0 2.0 +Description
diff --git a/doc/html/dihedral_fourier.html b/doc/html/dihedral_fourier.html index 1470ba7346..0feb09036b 100644 --- a/doc/html/dihedral_fourier.html +++ b/doc/html/dihedral_fourier.html @@ -131,16 +131,16 @@dihedral_style fourier/omp command
Syntax
--dihedral_style fourier -++dihedral_style fourier +Examples
--dihedral_style fourier -dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 -++dihedral_style fourier +dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 +Description
diff --git a/doc/html/dihedral_helix.html b/doc/html/dihedral_helix.html index b8d5653099..14a06fac03 100644 --- a/doc/html/dihedral_helix.html +++ b/doc/html/dihedral_helix.html @@ -131,16 +131,16 @@dihedral_style helix/omp command
Syntax
--dihedral_style helix -++dihedral_style helix +Examples
--dihedral_style helix -dihedral_coeff 1 80.0 100.0 40.0 -++dihedral_style helix +dihedral_coeff 1 80.0 100.0 40.0 +Description
diff --git a/doc/html/dihedral_multi_harmonic.html b/doc/html/dihedral_multi_harmonic.html index ec192b670e..c8f3b7b886 100644 --- a/doc/html/dihedral_multi_harmonic.html +++ b/doc/html/dihedral_multi_harmonic.html @@ -131,16 +131,16 @@dihedral_style multi/harmonic/omp command
Syntax
--dihedral_style multi/harmonic -++dihedral_style multi/harmonic +Examples
--dihedral_style multi/harmonic -dihedral_coeff 1 20 20 20 20 20 -++dihedral_style multi/harmonic +dihedral_coeff 1 20 20 20 20 20 +Description
diff --git a/doc/html/dihedral_nharmonic.html b/doc/html/dihedral_nharmonic.html index eb59b45627..eb35a50a58 100644 --- a/doc/html/dihedral_nharmonic.html +++ b/doc/html/dihedral_nharmonic.html @@ -131,16 +131,16 @@dihedral_style nharmonic/omp command
Syntax
--dihedral_style nharmonic -++dihedral_style nharmonic +Examples
--dihedral_style nharmonic -dihedral_coeff 3 10.0 20.0 30.0 -++dihedral_style nharmonic +dihedral_coeff 3 10.0 20.0 30.0 +Description
diff --git a/doc/html/dihedral_opls.html b/doc/html/dihedral_opls.html index fd7c9f1e4f..2f73119b58 100644 --- a/doc/html/dihedral_opls.html +++ b/doc/html/dihedral_opls.html @@ -137,18 +137,18 @@dihedral_style opls/omp command
Syntax
--dihedral_style opls -++dihedral_style opls +Examples
--dihedral_style opls -dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT -dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC -dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC -++dihedral_style opls +dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT +dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC +dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC +Description
diff --git a/doc/html/dihedral_quadratic.html b/doc/html/dihedral_quadratic.html index 3b490ae5d6..3cc35b63dd 100644 --- a/doc/html/dihedral_quadratic.html +++ b/doc/html/dihedral_quadratic.html @@ -131,16 +131,16 @@dihedral_style quadratic/omp command
Syntax
--dihedral_style quadratic -++dihedral_style quadratic +Examples
--dihedral_style quadratic -dihedral_coeff 100.0 80.0 -++dihedral_style quadratic +dihedral_coeff 100.0 80.0 +Description
diff --git a/doc/html/dihedral_spherical.html b/doc/html/dihedral_spherical.html index 3e38d2d8ca..1d9a9f7402 100644 --- a/doc/html/dihedral_spherical.html +++ b/doc/html/dihedral_spherical.html @@ -128,18 +128,18 @@dihedral_style spherical command
Syntax
--dihedral_style spherical -++dihedral_style spherical +Examples
--dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 -dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 & - 17.3 0 0.0 0 1 158 1 0 0.0 0 & - 15.1 0 0.0 0 0 0.0 0 1 167.3 1 -++dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 +dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 & + 17.3 0 0.0 0 1 158 1 0 0.0 0 & + 15.1 0 0.0 0 0 0.0 0 1 167.3 1 +Description
diff --git a/doc/html/dihedral_style.html b/doc/html/dihedral_style.html index c19d4a1a2e..9b21cd4640 100644 --- a/doc/html/dihedral_style.html +++ b/doc/html/dihedral_style.html @@ -128,20 +128,20 @@dihedral_style command
Syntax
--dihedral_style style -++dihedral_style style +
- style = none or hybrid or charmm or class2 or harmonic or helix or multi/harmonic or opls
Examples
--dihedral_style harmonic -dihedral_style multi/harmonic -dihedral_style hybrid harmonic charmm -++dihedral_style harmonic +dihedral_style multi/harmonic +dihedral_style hybrid harmonic charmm +Description
diff --git a/doc/html/fix_balance.html b/doc/html/fix_balance.html index 56beb5da2b..0415a0054b 100644 --- a/doc/html/fix_balance.html +++ b/doc/html/fix_balance.html @@ -432,8 +432,10 @@ will be duplicate nodes in the list. rectangle for each processor (1 to 4).For a 3d problem, the syntax is similar with 8 vertices listed for each processor, instead of 4, and “SQUARES” replaced by “CUBES”.
+
-Restart, fix_modify, output, run start/stop, minimize info:
++Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.
This fix computes a global scalar which is the imbalance factor diff --git a/doc/html/fix_bond_swap.html b/doc/html/fix_bond_swap.html index a3ae59400a..27a56cba19 100644 --- a/doc/html/fix_bond_swap.html +++ b/doc/html/fix_bond_swap.html @@ -229,9 +229,9 @@ quantities or the printing of unwrapped coordinates to a dump file.
This fix computes a temperature each time it is invoked for use by the Boltzmann criterion. To do this, the fix creates its own compute of style temp, as if this command had been issued:
--compute fix-ID_temp all temp -++compute fix-ID_temp all temp +See the compute temp command for details. Note that the ID of the new compute is the fix-ID with underscore + “temp” appended and the group for the new compute is “all”, so that the diff --git a/doc/html/fix_box_relax.html b/doc/html/fix_box_relax.html index e81bc87098..ea16211584 100644 --- a/doc/html/fix_box_relax.html +++ b/doc/html/fix_box_relax.html @@ -371,10 +371,10 @@ temperature is used to compute the kinetic contribution to the pressure, even though this is subsequently ignored by default. To do this, the fix creates its own computes of style “temp” and “pressure”, as if these commands had been issued:
--compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp virial -++compute fix-ID_temp group-ID temp +compute fix-ID_press group-ID pressure fix-ID_temp virial +See the compute temp and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is the same @@ -388,8 +388,10 @@ fix’s temperature or pressure via the or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this fix.
+
-Restart, fix_modify, output, run start/stop, minimize info:
++Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files.
The fix_modify temp and press options are supported by this fix. You can use them to assign a @@ -423,12 +425,12 @@ potential energy. This fix does not support the because that would result in double-counting of the fix energy in the minimization energy. Instead, the fix energy can be explicitly added to the potential energy using one of these two variants:
--variable emin equal pe+f_1 ---variable emin equal pe+f_1/atoms -+++variable emin equal pe+f_1 ++variable emin equal pe+f_1/atoms +No parameter of this fix can be used with the start/stop keywords of the run command.
This fix is invoked during energy minimization, but diff --git a/doc/html/fix_controller.html b/doc/html/fix_controller.html index e9e662670c..e6608bc009 100644 --- a/doc/html/fix_controller.html +++ b/doc/html/fix_controller.html @@ -141,13 +141,13 @@
Kd = derivative gain in PID equation (unitless) pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or v_name --c_ID = global scalar calculated by a compute with ID -c_ID[I] = Ith component of global vector calculated by a compute with ID -f_ID = global scalar calculated by a fix with ID -f_ID[I] = Ith component of global vector calculated by a fix with ID -v_name = value calculated by an equal-style variable with name -++c_ID = global scalar calculated by a compute with ID +c_ID[I] = Ith component of global vector calculated by a compute with ID +f_ID = global scalar calculated by a fix with ID +f_ID[I] = Ith component of global vector calculated by a fix with ID +v_name = value calculated by an equal-style variable with name +
- setpoint = desired value of process variable (same units as process variable)
- cvar = name of control variable
@@ -155,11 +155,11 @@ v_name = value calculated by an equal-style variable with nameExamples
--fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol -fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall -fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol -++fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol +fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall +fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol +Description
@@ -269,14 +269,14 @@ because the value of e_n-1 is not yet defined. compute or fix or the evaluation of a variable. In each case, the compute, fix, or variable must produce a global quantity, not a per-atom or local quantity. -If pvar begins with “c_”, a compute ID must follow which has been +
If pvar begins with “c_”, a compute ID must follow which has been previously defined in the input script and which generates a global scalar or vector. See the individual compute doc page for details. If no bracketed integer is appended, the scalar calculated by the compute is used. If a bracketed integer is appended, the Ith value of the vector calculated by the compute is used. Users can also write code for their own compute styles and add them to LAMMPS.
-If pvar begins with “f_”, a fix ID must follow which has been +
If pvar begins with “f_”, a fix ID must follow which has been previously defined in the input script and which generates a global scalar or vector. See the individual fix doc page for details. Note that some fixes only produce their values on certain @@ -285,7 +285,7 @@ references the values, or else an error results. If no bracketed integer is appended, the scalar calculated by the fix is used. If a bracketed integer is appended, the Ith value of the vector calculated by the fix is used. Users can also write code for their own fix style and add them to LAMMPS.
-If pvar begins with “v_”, a variable name must follow which has been +
If pvar begins with “v_”, a variable name must follow which has been previously defined in the input script. Only equal-style variables can be referenced. See the variable command for details. Note that variables of style equal define a formula which @@ -296,12 +296,14 @@ variable.
The target value setpoint for the process variable must be a numeric value, in whatever units pvar is defined for.
The control variable cvar must be the name of an internal-style variable previously defined in the input script. Note -that it is not specified with a “v_” prefix, just the name of the +that it is not specified with a “v_” prefix, just the name of the variable. It must be an internal-style variable, because this fix updates its value directly. Note that other commands can use an equal-style versus internal-style variable interchangeably.
+
-Restart, fix_modify, output, run start/stop, minimize info:
+++Restart, fix_modify, output, run start/stop, minimize info
Currenlty, no information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.
This fix produces a global vector with 3 values which can be accessed diff --git a/doc/html/fix_ehex.html b/doc/html/fix_ehex.html index a753adb554..f1cc66f404 100644 --- a/doc/html/fix_ehex.html +++ b/doc/html/fix_ehex.html @@ -262,8 +262,10 @@ be on the order of \(10^{-7}\) for relatively large temperature gradients. A higher precision can be achieved by decreasing the timestep.
-Restart, fix_modify, output, run start/stop, minimize info:
++Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix.
No parameter of this fix can be used with the start/stop keywords of diff --git a/doc/html/fix_gld.html b/doc/html/fix_gld.html index 96beaab03f..aba80b6a9d 100644 --- a/doc/html/fix_gld.html +++ b/doc/html/fix_gld.html @@ -128,9 +128,9 @@
fix gld command
Syntax
--fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ... -++fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ... +
- ID, group-ID are documented in fix command
- gld = style name of this fix command
diff --git a/doc/html/fix_lb_fluid.html b/doc/html/fix_lb_fluid.html index fadee5ceb3..51eefacda2 100644 --- a/doc/html/fix_lb_fluid.html +++ b/doc/html/fix_lb_fluid.html @@ -374,8 +374,10 @@ screen every N timesteps. test runs, see Mackay et al.. Please include a citation to this paper if the lb_fluid fix is used in work contributing to published research. +
-Restart, fix_modify, output, run start/stop, minimize info:
++Restart, fix_modify, output, run start/stop, minimize info
Due to the large size of the fluid data, this fix writes it’s own binary restart files, if requested, independent of the main LAMMPS binary restart files; no information about lb_fluid diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html index 8cbee0b46f..ff55e4e302 100644 --- a/doc/html/fix_nh.html +++ b/doc/html/fix_nh.html @@ -158,9 +158,9 @@
fix nph/omp command
Syntax
--fix ID group-ID style_name keyword value ... -++fix ID group-ID style_name keyword value ... +
- ID, group-ID are documented in fix command
- style_name = nvt or npt or nph
@@ -508,14 +508,14 @@ thermostatting and barostatting.These fixes compute a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp” and “pressure”, as if one of these two sets of commands had been issued:
--compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp ---compute fix-ID_temp all temp -compute fix-ID_press all pressure fix-ID_temp -+++compute fix-ID_temp group-ID temp +compute fix-ID_press group-ID pressure fix-ID_temp ++compute fix-ID_temp all temp +compute fix-ID_press all pressure fix-ID_temp +See the compute temp and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”. For fix nvt, the group for the new computes @@ -606,8 +606,10 @@ by including their suffix, or you can use the suffix command in your input script.
See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.
+
-Restart, fix_modify, output, run start/stop, minimize info:
++Restart, fix_modify, output, run start/stop, minimize info
These fixes writes the state of all the thermostat and barostat variables to binary restart files. See the read_restart command for info on how to re-specify diff --git a/doc/html/fix_nphug.html b/doc/html/fix_nphug.html index 85dd234fe3..da32f6307b 100644 --- a/doc/html/fix_nphug.html +++ b/doc/html/fix_nphug.html @@ -229,14 +229,14 @@ controlled by another fix - e.g. by -compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp - -
-compute fix-ID_temp all temp -compute fix-ID_press all pressure fix-ID_temp -+++compute fix-ID_temp group-ID temp +compute fix-ID_press group-ID pressure fix-ID_temp ++compute fix-ID_temp all temp +compute fix-ID_press all pressure fix-ID_temp +See the compute temp and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”. The group for @@ -266,8 +266,10 @@ by including their suffix, or you can use the suffix command in your input script.
See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively.
+
-Restart, fix_modify, output, run start/stop, minimize info:
+++Restart, fix_modify, output, run start/stop, minimize info
This fix writes the values of E0, V0, and P0, as well as the state of all the thermostat and barostat variables to binary restart files. See the @@ -291,7 +293,7 @@ compute temperature on a subset of atoms.
The fix_modify energy option is supported by these fixes to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system’s potential energy as part of -thermodynamic output. Either way, this energy is *not* +thermodynamic output. Either way, this energy is not included in the definition of internal energy E when calculating the value of Delta in the above equation.
These fixes compute a global scalar and a global vector of quantities, diff --git a/doc/html/fix_orient.html b/doc/html/fix_orient.html index 9b01605d28..74dd4d3477 100644 --- a/doc/html/fix_orient.html +++ b/doc/html/fix_orient.html @@ -232,7 +232,9 @@ symmetry, so the list must include one from each pair of equal-and-opposite neighbors. A pair of orientation files for a Sigma=5 tilt boundary are shown below. A tutorial that can help for writing the orientation files is given in (Wicaksono2)
-Restart, fix_modify, output, run start/stop, minimize info:
++Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files.
The fix_modify energy option is supported by this fix to add the potential energy of atom interactions with the grain diff --git a/doc/html/fix_pimd.html b/doc/html/fix_pimd.html index 545be26b57..57ee90e294 100644 --- a/doc/html/fix_pimd.html +++ b/doc/html/fix_pimd.html @@ -232,9 +232,9 @@ ring.
To run a PIMD simulation with M quasi-beads in each ring polymer using N MPI tasks for each partition’s domain-decomposition, you would use P = MxN processors (cores) and run the simulation as follows:
--mpirun -np P lmp_mpi -partition MxN -in script -++mpirun -np P lmp_mpi -partition MxN -in script +Note that in the LAMMPS input script for a multi-partition simulation, it is often very useful to define a uloop-style variable such as
variable ibead uloop M pad @@ -243,11 +243,11 @@ it is often very useful to define a -dump dcd all dcd 10 system_${ibead}.dcd ++dump dcd all dcd 10 system_${ibead}.dcd restart 1000 system_${ibead}.restart1 system_${ibead}.restart2 read_restart system_${ibead}.restart2 -+Restrictions
diff --git a/doc/html/fix_qbmsst.html b/doc/html/fix_qbmsst.html index f3dca0ee47..1fb67f4518 100644 --- a/doc/html/fix_qbmsst.html +++ b/doc/html/fix_qbmsst.html @@ -157,10 +157,10 @@Examples
--fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units) -fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units) -++fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units) +fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units) +Two example input scripts are given, including shocked alpha quartz and shocked liquid methane. The input script first equilibrate an initial state with the quantum thermal bath at the target temperature @@ -242,8 +242,10 @@ thermal bath and the system before shock loading.
For all pressure styles, the simulation box stays orthorhombic in shape. Parrinello-Rahman boundary conditions (tilted box) are supported by LAMMPS, but are not implemented for QBMSST.
+
-Restart, fix_modify, output, run start/stop, minimize info:
++Restart, fix_modify, output, run start/stop, minimize info
Because the state of the random number generator is not written to binary restart files, this fix cannot be restarted “exactly” in an uninterrupted fashion. However, in a statistical @@ -269,16 +271,16 @@ headers, the following LAMMPS commands are suggested. Here the fix_modify energy command is also enabled to allow the thermo keyword etotal to print the quantity <i>etot</i>. See also the thermo_style command.
--fix fix_id all msst z -fix_modify fix_id energy yes -variable dhug equal f_fix_id[1] -variable dray equal f_fix_id[2] -variable lgr_vel equal f_fix_id[3] -variable lgr_pos equal f_fix_id[4] -variable T_qm equal f_fix_id[5] -thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id -++fix fix_id all msst z +fix_modify fix_id energy yes +variable dhug equal f_fix_id[1] +variable dray equal f_fix_id[2] +variable lgr_vel equal f_fix_id[3] +variable lgr_pos equal f_fix_id[4] +variable T_qm equal f_fix_id[5] +thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id +The global scalar under the entry f_fix_id is the quantity of thermo energy as an extra part of <i>etot</i>. This global scalar and the vector of 5 quantities can be accessed by various output commands. It is worth noting that the diff --git a/doc/html/fix_restrain.html b/doc/html/fix_restrain.html index ef8c9949c2..3612f2e3fd 100644 --- a/doc/html/fix_restrain.html +++ b/doc/html/fix_restrain.html @@ -165,15 +165,27 @@ fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5
Description
Restrain the motion of the specified sets of atoms by making them part of a bond or angle or dihedral interaction whose strength can vary -over time during a simulation. This is functionally equivalent to +over time during a simulation. This is functionally similar to creating a bond or angle or dihedral for the same atoms in a data file, as specified by the read_data command, albeit -with a time-varying pre-factor coefficient. For the purpose of -forcefield parameter-fitting or mapping a molecular potential energy -surface, this fix reduces the hassle and risk associated with -modifying data files. In other words, use this fix to temporarily -force a molecule to adopt a particular conformation. To create a -permanent bond or angle or dihedral, you should modify the data file.
+with a time-varying pre-factor coefficient, and except for exclusion +rules, as explained below. +For the purpose of forcefield parameter-fitting or mapping a molecular +potential energy surface, this fix reduces the hassle and risk +associated with modifying data files. In other words, use this fix to +temporarily force a molecule to adopt a particular conformation. To +create a permanent bond or angle or dihedral, you should modify the +data file.
++Note
+Adding a bond/angle/dihedral with this command does not apply +the exclusion rules and weighting factors specified by the +special_bonds command to atoms in the restraint +that are now bonded (1-2,1-3,1-4 neighbors) as a result. If they are +close enough to interact in a pair_style sense +(non-bonded interaction), then the bond/angle/dihedral restraint +interaction will simply be superposed on top of that interaction.
+The group-ID specified by this fix is ignored.
The second example above applies a restraint to hold the dihedral angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant diff --git a/doc/html/fix_rx.html b/doc/html/fix_rx.html index 6d337133f8..b39fe17f46 100644 --- a/doc/html/fix_rx.html +++ b/doc/html/fix_rx.html @@ -147,13 +147,13 @@
Examples
--fix 1 all rx kinetics.rx none dense lammps_rk4 -fix 1 all rx kinetics.rx none sparse lammps_rk4 1 -fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10 -fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1 -++fix 1 all rx kinetics.rx none dense lammps_rk4 +fix 1 all rx kinetics.rx none sparse lammps_rk4 1 +fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10 +fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 +fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1 ++Description
@@ -271,7 +271,7 @@ temperature exponent n, and the activation energy Ea. are used by the fix eos/table/rx command to define the thermodynamic properties of each species. Furthermore, the number of species molecules (i.e., concentration) can be specified -either with the set command using the “d_” prefix or by +either with the set command using the “d_” prefix or by reading directly the concentrations from a data file. For the latter case, the read_data command with the fix keyword should be specified, where the fix-ID will be the “fix rx`ID with a <SPECIES”>`_ suffix, e.g. diff --git a/doc/html/fix_shake.html b/doc/html/fix_shake.html index 6c279062d0..7cfb03e019 100644 --- a/doc/html/fix_shake.html +++ b/doc/html/fix_shake.html @@ -289,8 +289,10 @@ the RATTLE constraints. You can check whether the constraints work correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp to 1 and recompiling LAMMPS.
-Restart, fix_modify, output, run start/stop, minimize info:
+++Restart, fix_modify, output, run start/stop, minimize info
No information about these fixes is written to binary restart files. None of the fix_modify options are relevant to these fixes. No global or per-atom quantities are stored by these fixes for access by various output commands. No parameter of these fixes diff --git a/doc/html/fix_spring_rg.html b/doc/html/fix_spring_rg.html index 8cb641326c..aeaa3bece4 100644 --- a/doc/html/fix_spring_rg.html +++ b/doc/html/fix_spring_rg.html @@ -166,7 +166,9 @@ the mass of the entire group. Note that K is thus a force constant for the aggregate force on the group of atoms, not a per-atom force.
If RG0 is specified as NULL, then the RG of the group is computed at the time the fix is specified, and that value is used as the target.
-Restart, fix_modify, output, run start/stop, minimize info:
++Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_ti_rs.html b/doc/html/fix_ti_rs.html index f298fc952d..311cabb702 100644 --- a/doc/html/fix_ti_rs.html +++ b/doc/html/fix_ti_rs.html @@ -128,9 +128,9 @@
fix ti/rs command
+Syntax
--fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ... -++fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ... +
- ID, group-ID are documented in fix command
- ti/rs = style name of this fix command
@@ -198,7 +198,9 @@ scaling is faster at temperatures closer to the initial temperature of the procedure.An example script using this command is provided in the examples/USER/misc/ti directory.
-Restart, fix_modify, output, run start/stop, minimize info:
+++Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files.
This fix computes a global vector quantitie which can be accessed by various output commands. The vector has diff --git a/doc/html/fix_ti_spring.html b/doc/html/fix_ti_spring.html index e7d63d947a..a0a3a6db23 100644 --- a/doc/html/fix_ti_spring.html +++ b/doc/html/fix_ti_spring.html @@ -128,9 +128,9 @@
fix ti/spring command
-Syntax
--fix ID group-ID ti/spring K t_switch t_equil keyword value ... -++fix ID group-ID ti/spring K t_switch t_equil keyword value ... +
- ID, group-ID are documented in fix command
- ti/spring = style name of this fix command
@@ -205,7 +205,9 @@ issues with the canonical sampling of harmonic degrees of freedom (notice that the chain option will NOT solve this problem). The Langevin thermostat (fix langevin) works fine.Restart, fix_modify, output, run start/stop, minimize info:
+++Restart, fix_modify, output, run start/stop, minimize info
This fix writes the original coordinates of tethered atoms to binary restart files, so that the spring effect will be the same in a restarted simulation. See the read restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of diff --git a/doc/html/fix_ttm.html b/doc/html/fix_ttm.html index 1b12323895..af630d2964 100644 --- a/doc/html/fix_ttm.html +++ b/doc/html/fix_ttm.html @@ -131,50 +131,50 @@
fix ttm/mod command
Syntax
--fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile -fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile -++fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile +fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile +-
- ID, group-ID are documented in fix command
- style = ttm or ttm_mod
- seed = random number seed to use for white noise (positive integer)
- remaining arguments for fix ttm:
-C_e = electronic specific heat (energy/(electron*temperature) units) -rho_e = electronic density (electrons/volume units) -kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units) -gamma_p = friction coefficient due to electron-ion interactions (mass/time units) -gamma_s = friction coefficient due to electronic stopping (mass/time units) -v_0 = electronic stopping critical velocity (velocity units) -Nx = number of thermal solve grid points in the x-direction (positive integer) -Ny = number of thermal solve grid points in the y-direction (positive integer) -Nz = number of thermal solve grid points in the z-direction (positive integer) -T_infile = filename to read initial electronic temperature from -N = dump TTM temperatures every this many timesteps, 0 = no dump -T_outfile = filename to write TTM temperatures to (only needed if N > 0) -++C_e = electronic specific heat (energy/(electron*temperature) units) +rho_e = electronic density (electrons/volume units) +kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units) +gamma_p = friction coefficient due to electron-ion interactions (mass/time units) +gamma_s = friction coefficient due to electronic stopping (mass/time units) +v_0 = electronic stopping critical velocity (velocity units) +Nx = number of thermal solve grid points in the x-direction (positive integer) +Ny = number of thermal solve grid points in the y-direction (positive integer) +Nz = number of thermal solve grid points in the z-direction (positive integer) +T_infile = filename to read initial electronic temperature from +N = dump TTM temperatures every this many timesteps, 0 = no dump +T_outfile = filename to write TTM temperatures to (only needed if N > 0) +-
- remaining arguments for fix ttm/mod:
-init_file = file with the parameters to TTM -Nx = number of thermal solve grid points in the x-direction (positive integer) -Ny = number of thermal solve grid points in the y-direction (positive integer) -Nz = number of thermal solve grid points in the z-direction (positive integer) -T_infile = filename to read initial electronic temperature from -N = dump TTM temperatures every this many timesteps, 0 = no dump -T_outfile = filename to write TTM temperatures to (only needed if N > 0) -++init_file = file with the parameters to TTM +Nx = number of thermal solve grid points in the x-direction (positive integer) +Ny = number of thermal solve grid points in the y-direction (positive integer) +Nz = number of thermal solve grid points in the z-direction (positive integer) +T_infile = filename to read initial electronic temperature from +N = dump TTM temperatures every this many timesteps, 0 = no dump +T_outfile = filename to write TTM temperatures to (only needed if N > 0) +Examples
--fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out -fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out -fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out -++fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out +fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out +fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out +Description
@@ -330,32 +330,34 @@ is calculated asThe fix ttm/mod parameter file init_file has the following syntax/ Every line with the odd number is considered as a comment and ignored. The lines with the even numbers are treated as follows:
--a_0, energy/(temperature*electron) units -a_1, energy/(temperature^2*electron) units -a_2, energy/(temperature^3*electron) units -a_3, energy/(temperature^4*electron) units -a_4, energy/(temperature^5*electron) units -C_0, energy/(temperature*electron) units -A, 1/temperature units -rho_e, electrons/volume units -D_e, length^2/time units -gamma_p, mass/time units -gamma_s, mass/time units -v_0, length/time units -I_0, energy/(time*length^2) units -lsurface, electron grid units (positive integer) -rsurface, electron grid units (positive integer) -l_skin, length units -tau, time units -B, dimensionless -lambda, length units -n_ion, ions/volume units -surface_movement: 0 to disable tracking of surface motion, 1 to enable -T_e_min, temperature units -+++a_0, energy/(temperature*electron) units +a_1, energy/(temperature^2*electron) units +a_2, energy/(temperature^3*electron) units +a_3, energy/(temperature^4*electron) units +a_4, energy/(temperature^5*electron) units +C_0, energy/(temperature*electron) units +A, 1/temperature units +rho_e, electrons/volume units +D_e, length^2/time units +gamma_p, mass/time units +gamma_s, mass/time units +v_0, length/time units +I_0, energy/(time*length^2) units +lsurface, electron grid units (positive integer) +rsurface, electron grid units (positive integer) +l_skin, length units +tau, time units +B, dimensionless +lambda, length units +n_ion, ions/volume units +surface_movement: 0 to disable tracking of surface motion, 1 to enable +T_e_min, temperature units +
-Restart, fix_modify, output, run start/stop, minimize info:
++Restart, fix_modify, output, run start/stop, minimize info
These fixes write the state of the electronic subsystem and the energy exchange between the subsystems to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a diff --git a/doc/html/fix_wall.html b/doc/html/fix_wall.html index 0a1d123b92..8f3ac46551 100644 --- a/doc/html/fix_wall.html +++ b/doc/html/fix_wall.html @@ -179,12 +179,12 @@ args = coord epsilon sigma cutoff
Examples
--fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box -fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5 -fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5 -fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 -++fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box +fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5 +fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5 +fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 +Description
@@ -321,22 +321,22 @@ want. in a time-dependent fashion using equal-style variables. The wall interaction parameters (epsilon, sigma) could be varied with additional variable definitions. --variable ramp equal ramp(0,10) -fix 1 all wall xlo v_ramp 1.0 1.0 2.5 ---variable linear equal vdisplace(0,20) -fix 1 all wall xlo v_linear 1.0 1.0 2.5 ---variable wiggle equal swiggle(0.0,5.0,3.0) -fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 ---variable wiggle equal cwiggle(0.0,5.0,3.0) -fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 -+++variable ramp equal ramp(0,10) +fix 1 all wall xlo v_ramp 1.0 1.0 2.5 +++variable linear equal vdisplace(0,20) +fix 1 all wall xlo v_linear 1.0 1.0 2.5 +++variable wiggle equal swiggle(0.0,5.0,3.0) +fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 ++variable wiggle equal cwiggle(0.0,5.0,3.0) +fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 +The ramp(lo,hi) function adjusts the wall position linearly from lo to hi over the course of a run. The vdisplace(c0,velocity) function does something similar using the equation position = c0 + velocity*delta, @@ -344,18 +344,20 @@ where delta is the elapsed time.
The swiggle(c0,A,period) function causes the wall position to oscillate sinusoidally according to this equation, where omega = 2 PI / period:
--position = c0 + A sin(omega*delta) -++position = c0 + A sin(omega*delta) +The cwiggle(c0,A,period) function causes the wall position to oscillate sinusoidally according to this equation, which will have an initial wall velocity of 0.0, and thus may impose a gentler perturbation on the particles:
--position = c0 + A (1 - cos(omega*delta)) -+++position = c0 + A (1 - cos(omega*delta)) +
-Restart, fix_modify, output, run start/stop, minimize info:
++-Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files.
The fix_modify energy option is supported by this fix to add the energy of interaction between atoms and each wall to diff --git a/doc/html/fix_wall_region.html b/doc/html/fix_wall_region.html index ba645d66ef..4f24bee99a 100644 --- a/doc/html/fix_wall_region.html +++ b/doc/html/fix_wall_region.html @@ -280,7 +280,9 @@ and does not blow up as r -> 0, but you must use a large enough epsilon that particles always reamin on the correct side of the region surface (r > 0).
Restart, fix_modify, output, run start/stop, minimize info:
++Restart, fix_modify, output, run start/stop, minimize info
No information about this fix is written to binary restart files.
The fix_modify energy option is supported by this fix to add the energy of interaction between atoms and the wall to the diff --git a/doc/html/genindex.html b/doc/html/genindex.html index b40e27bf00..0e140ad1a1 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -156,93 +156,93 @@
![dihedral_style charmm/omp command Syntax - -dihedral_style charmm - +dihedral_style charmm + + Examples - -dihedral_style charmm -dihedral_coeff 1 0.2 1 180 1.0 -dihedral_coeff 2 1.8 1 0 1.0 -dihedral_coeff 1 3.1 2 180 0.5 - +dihedral_style charmm +dihedral_coeff 1 0.2 1 180 1.0 +dihedral_coeff 2 1.8 1 0 1.0 +dihedral_coeff 1 3.1 2 180 0.5 + + Description diff --git a/doc/html/dihedral_class2.html b/doc/html/dihedral_class2.html index e9556733e2..40f10f1e74 100644 --- a/doc/html/dihedral_class2.html +++ b/doc/html/dihedral_class2.html @@ -131,21 +131,21 @@ dihedral_style class2/omp command Syntax - -dihedral_style class2 - +dihedral_style class2 + + Examples - -dihedral_style class2 -dihedral_coeff 1 100 75 100 70 80 60 -dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 -dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010 -dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 -dihedral_coeff * aat -13.5271 110.2453 105.1270 -dihedral_coeff * bb13 0.0 1.0119 1.1010 - +dihedral_style class2 +dihedral_coeff 1 100 75 100 70 80 60 +dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 +dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010 +dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 +dihedral_coeff * aat -13.5271 110.2453 105.1270 +dihedral_coeff * bb13 0.0 1.0119 1.1010 + + Description diff --git a/doc/html/dihedral_cosine_shift_exp.html b/doc/html/dihedral_cosine_shift_exp.html index 1cc73331be..b6e718bce8 100644 --- a/doc/html/dihedral_cosine_shift_exp.html +++ b/doc/html/dihedral_cosine_shift_exp.html @@ -131,16 +131,16 @@ dihedral_style cosine/shift/exp/omp command Syntax - -dihedral_style cosine/shift/exp - +dihedral_style cosine/shift/exp + + Examples - -dihedral_style cosine/shift/exp -dihedral_coeff 1 10.0 45.0 2.0 - +dihedral_style cosine/shift/exp +dihedral_coeff 1 10.0 45.0 2.0 + + Description diff --git a/doc/html/dihedral_fourier.html b/doc/html/dihedral_fourier.html index 1470ba7346..0feb09036b 100644 --- a/doc/html/dihedral_fourier.html +++ b/doc/html/dihedral_fourier.html @@ -131,16 +131,16 @@ dihedral_style fourier/omp command Syntax - -dihedral_style fourier - +dihedral_style fourier + + Examples - -dihedral_style fourier -dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 - +dihedral_style fourier +dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0 + + Description diff --git a/doc/html/dihedral_helix.html b/doc/html/dihedral_helix.html index b8d5653099..14a06fac03 100644 --- a/doc/html/dihedral_helix.html +++ b/doc/html/dihedral_helix.html @@ -131,16 +131,16 @@ dihedral_style helix/omp command Syntax - -dihedral_style helix - +dihedral_style helix + + Examples - -dihedral_style helix -dihedral_coeff 1 80.0 100.0 40.0 - +dihedral_style helix +dihedral_coeff 1 80.0 100.0 40.0 + + Description diff --git a/doc/html/dihedral_multi_harmonic.html b/doc/html/dihedral_multi_harmonic.html index ec192b670e..c8f3b7b886 100644 --- a/doc/html/dihedral_multi_harmonic.html +++ b/doc/html/dihedral_multi_harmonic.html @@ -131,16 +131,16 @@ dihedral_style multi/harmonic/omp command Syntax - -dihedral_style multi/harmonic - +dihedral_style multi/harmonic + + Examples - -dihedral_style multi/harmonic -dihedral_coeff 1 20 20 20 20 20 - +dihedral_style multi/harmonic +dihedral_coeff 1 20 20 20 20 20 + + Description diff --git a/doc/html/dihedral_nharmonic.html b/doc/html/dihedral_nharmonic.html index eb59b45627..eb35a50a58 100644 --- a/doc/html/dihedral_nharmonic.html +++ b/doc/html/dihedral_nharmonic.html @@ -131,16 +131,16 @@ dihedral_style nharmonic/omp command Syntax - -dihedral_style nharmonic - +dihedral_style nharmonic + + Examples - -dihedral_style nharmonic -dihedral_coeff 3 10.0 20.0 30.0 - +dihedral_style nharmonic +dihedral_coeff 3 10.0 20.0 30.0 + + Description diff --git a/doc/html/dihedral_opls.html b/doc/html/dihedral_opls.html index fd7c9f1e4f..2f73119b58 100644 --- a/doc/html/dihedral_opls.html +++ b/doc/html/dihedral_opls.html @@ -137,18 +137,18 @@ dihedral_style opls/omp command Syntax - -dihedral_style opls - +dihedral_style opls + + Examples - -dihedral_style opls -dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT -dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC -dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC - +dihedral_style opls +dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT +dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC +dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC + + Description diff --git a/doc/html/dihedral_quadratic.html b/doc/html/dihedral_quadratic.html index 3b490ae5d6..3cc35b63dd 100644 --- a/doc/html/dihedral_quadratic.html +++ b/doc/html/dihedral_quadratic.html @@ -131,16 +131,16 @@ dihedral_style quadratic/omp command Syntax - -dihedral_style quadratic - +dihedral_style quadratic + + Examples - -dihedral_style quadratic -dihedral_coeff 100.0 80.0 - +dihedral_style quadratic +dihedral_coeff 100.0 80.0 + + Description diff --git a/doc/html/dihedral_spherical.html b/doc/html/dihedral_spherical.html index 3e38d2d8ca..1d9a9f7402 100644 --- a/doc/html/dihedral_spherical.html +++ b/doc/html/dihedral_spherical.html @@ -128,18 +128,18 @@ dihedral_style spherical command Syntax - -dihedral_style spherical - +dihedral_style spherical + + Examples - -dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 -dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 & - 17.3 0 0.0 0 1 158 1 0 0.0 0 & - 15.1 0 0.0 0 0 0.0 0 1 167.3 1 - +dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 +dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 & + 17.3 0 0.0 0 1 158 1 0 0.0 0 & + 15.1 0 0.0 0 0 0.0 0 1 167.3 1 + + Description diff --git a/doc/html/dihedral_style.html b/doc/html/dihedral_style.html index c19d4a1a2e..9b21cd4640 100644 --- a/doc/html/dihedral_style.html +++ b/doc/html/dihedral_style.html @@ -128,20 +128,20 @@ dihedral_style command Syntax - -dihedral_style style - +dihedral_style style + + style = none or hybrid or charmm or class2 or harmonic or helix or multi/harmonic or opls Examples - -dihedral_style harmonic -dihedral_style multi/harmonic -dihedral_style hybrid harmonic charmm - +dihedral_style harmonic +dihedral_style multi/harmonic +dihedral_style hybrid harmonic charmm + + Description diff --git a/doc/html/fix_balance.html b/doc/html/fix_balance.html index 56beb5da2b..0415a0054b 100644 --- a/doc/html/fix_balance.html +++ b/doc/html/fix_balance.html @@ -432,8 +432,10 @@ will be duplicate nodes in the list. rectangle for each processor (1 to 4). For a 3d problem, the syntax is similar with 8 vertices listed for each processor, instead of 4, and “SQUARES” replaced by “CUBES”. + -Restart, fix_modify, output, run start/stop, minimize info: + +Restart, fix_modify, output, run start/stop, minimize info No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. This fix computes a global scalar which is the imbalance factor diff --git a/doc/html/fix_bond_swap.html b/doc/html/fix_bond_swap.html index a3ae59400a..27a56cba19 100644 --- a/doc/html/fix_bond_swap.html +++ b/doc/html/fix_bond_swap.html @@ -229,9 +229,9 @@ quantities or the printing of unwrapped coordinates to a dump file. This fix computes a temperature each time it is invoked for use by the Boltzmann criterion. To do this, the fix creates its own compute of style temp, as if this command had been issued: - -compute fix-ID_temp all temp - +compute fix-ID_temp all temp + + See the compute temp command for details. Note that the ID of the new compute is the fix-ID with underscore + “temp” appended and the group for the new compute is “all”, so that the diff --git a/doc/html/fix_box_relax.html b/doc/html/fix_box_relax.html index e81bc87098..ea16211584 100644 --- a/doc/html/fix_box_relax.html +++ b/doc/html/fix_box_relax.html @@ -371,10 +371,10 @@ temperature is used to compute the kinetic contribution to the pressure, even though this is subsequently ignored by default. To do this, the fix creates its own computes of style “temp” and “pressure”, as if these commands had been issued: - -compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp virial - +compute fix-ID_temp group-ID temp +compute fix-ID_press group-ID pressure fix-ID_temp virial + + See the compute temp and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is the same @@ -388,8 +388,10 @@ fix’s temperature or pressure via the or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this fix. + -Restart, fix_modify, output, run start/stop, minimize info: + +Restart, fix_modify, output, run start/stop, minimize info No information about this fix is written to binary restart files. The fix_modify temp and press options are supported by this fix. You can use them to assign a @@ -423,12 +425,12 @@ potential energy. This fix does not support the because that would result in double-counting of the fix energy in the minimization energy. Instead, the fix energy can be explicitly added to the potential energy using one of these two variants: - -variable emin equal pe+f_1 - - -variable emin equal pe+f_1/atoms - +variable emin equal pe+f_1 + + +variable emin equal pe+f_1/atoms + + No parameter of this fix can be used with the start/stop keywords of the run command. This fix is invoked during energy minimization, but diff --git a/doc/html/fix_controller.html b/doc/html/fix_controller.html index e9e662670c..e6608bc009 100644 --- a/doc/html/fix_controller.html +++ b/doc/html/fix_controller.html @@ -141,13 +141,13 @@ Kd = derivative gain in PID equation (unitless) pvar = process variable of form c_ID, c_ID[I], f_ID, f_ID[I], or v_name - -c_ID = global scalar calculated by a compute with ID -c_ID[I] = Ith component of global vector calculated by a compute with ID -f_ID = global scalar calculated by a fix with ID -f_ID[I] = Ith component of global vector calculated by a fix with ID -v_name = value calculated by an equal-style variable with name - +c_ID = global scalar calculated by a compute with ID +c_ID[I] = Ith component of global vector calculated by a compute with ID +f_ID = global scalar calculated by a fix with ID +f_ID[I] = Ith component of global vector calculated by a fix with ID +v_name = value calculated by an equal-style variable with name + + setpoint = desired value of process variable (same units as process variable) cvar = name of control variable @@ -155,11 +155,11 @@ v_name = value calculated by an equal-style variable with name Examples - -fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol -fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall -fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol - +fix 1 all controller 100 1.0 0.5 0.0 0.0 c_thermo_temp 1.5 tcontrol +fix 1 all controller 100 0.2 0.5 0 100.0 v_pxxwall 1.01325 xwall +fix 1 all controller 10000 0.2 0.5 0 2000 v_avpe -3.785 tcontrol + + Description @@ -269,14 +269,14 @@ because the value of e_n-1 is not yet defined. compute or fix or the evaluation of a variable. In each case, the compute, fix, or variable must produce a global quantity, not a per-atom or local quantity. -If pvar begins with “c_”, a compute ID must follow which has been +If pvar begins with “c_”, a compute ID must follow which has been previously defined in the input script and which generates a global scalar or vector. See the individual compute doc page for details. If no bracketed integer is appended, the scalar calculated by the compute is used. If a bracketed integer is appended, the Ith value of the vector calculated by the compute is used. Users can also write code for their own compute styles and add them to LAMMPS. -If pvar begins with “f_”, a fix ID must follow which has been +If pvar begins with “f_”, a fix ID must follow which has been previously defined in the input script and which generates a global scalar or vector. See the individual fix doc page for details. Note that some fixes only produce their values on certain @@ -285,7 +285,7 @@ references the values, or else an error results. If no bracketed integer is appended, the scalar calculated by the fix is used. If a bracketed integer is appended, the Ith value of the vector calculated by the fix is used. Users can also write code for their own fix style and add them to LAMMPS. -If pvar begins with “v_”, a variable name must follow which has been +If pvar begins with “v_”, a variable name must follow which has been previously defined in the input script. Only equal-style variables can be referenced. See the variable command for details. Note that variables of style equal define a formula which @@ -296,12 +296,14 @@ variable. The target value setpoint for the process variable must be a numeric value, in whatever units pvar is defined for. The control variable cvar must be the name of an internal-style variable previously defined in the input script. Note -that it is not specified with a “v_” prefix, just the name of the +that it is not specified with a “v_” prefix, just the name of the variable. It must be an internal-style variable, because this fix updates its value directly. Note that other commands can use an equal-style versus internal-style variable interchangeably. + -Restart, fix_modify, output, run start/stop, minimize info: + +Restart, fix_modify, output, run start/stop, minimize info Currenlty, no information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. This fix produces a global vector with 3 values which can be accessed diff --git a/doc/html/fix_ehex.html b/doc/html/fix_ehex.html index a753adb554..f1cc66f404 100644 --- a/doc/html/fix_ehex.html +++ b/doc/html/fix_ehex.html @@ -262,8 +262,10 @@ be on the order of \(10^{-7}\) for relatively large temperature gradients. A higher precision can be achieved by decreasing the timestep. + -Restart, fix_modify, output, run start/stop, minimize info: + +Restart, fix_modify, output, run start/stop, minimize info No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No parameter of this fix can be used with the start/stop keywords of diff --git a/doc/html/fix_gld.html b/doc/html/fix_gld.html index 96beaab03f..aba80b6a9d 100644 --- a/doc/html/fix_gld.html +++ b/doc/html/fix_gld.html @@ -128,9 +128,9 @@ fix gld command Syntax - -fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ... - +fix ID group-ID gld Tstart Tstop N_k seed series c_1 tau_1 ... c_N_k tau_N_k keyword values ... + + ID, group-ID are documented in fix command gld = style name of this fix command diff --git a/doc/html/fix_lb_fluid.html b/doc/html/fix_lb_fluid.html index fadee5ceb3..51eefacda2 100644 --- a/doc/html/fix_lb_fluid.html +++ b/doc/html/fix_lb_fluid.html @@ -374,8 +374,10 @@ screen every N timesteps. test runs, see Mackay et al.. Please include a citation to this paper if the lb_fluid fix is used in work contributing to published research. + -Restart, fix_modify, output, run start/stop, minimize info: + +Restart, fix_modify, output, run start/stop, minimize info Due to the large size of the fluid data, this fix writes it’s own binary restart files, if requested, independent of the main LAMMPS binary restart files; no information about lb_fluid diff --git a/doc/html/fix_nh.html b/doc/html/fix_nh.html index 8cbee0b46f..ff55e4e302 100644 --- a/doc/html/fix_nh.html +++ b/doc/html/fix_nh.html @@ -158,9 +158,9 @@ fix nph/omp command Syntax - -fix ID group-ID style_name keyword value ... - +fix ID group-ID style_name keyword value ... + + ID, group-ID are documented in fix command style_name = nvt or npt or nph @@ -508,14 +508,14 @@ thermostatting and barostatting. These fixes compute a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp” and “pressure”, as if one of these two sets of commands had been issued: - -compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp - - -compute fix-ID_temp all temp -compute fix-ID_press all pressure fix-ID_temp - +compute fix-ID_temp group-ID temp +compute fix-ID_press group-ID pressure fix-ID_temp + + +compute fix-ID_temp all temp +compute fix-ID_press all pressure fix-ID_temp + + See the compute temp and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”. For fix nvt, the group for the new computes @@ -606,8 +606,10 @@ by including their suffix, or you can use the suffix command in your input script. See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively. + -Restart, fix_modify, output, run start/stop, minimize info: + +Restart, fix_modify, output, run start/stop, minimize info These fixes writes the state of all the thermostat and barostat variables to binary restart files. See the read_restart command for info on how to re-specify diff --git a/doc/html/fix_nphug.html b/doc/html/fix_nphug.html index 85dd234fe3..da32f6307b 100644 --- a/doc/html/fix_nphug.html +++ b/doc/html/fix_nphug.html @@ -229,14 +229,14 @@ controlled by another fix - e.g. by -compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp - - -compute fix-ID_temp all temp -compute fix-ID_press all pressure fix-ID_temp - +compute fix-ID_temp group-ID temp +compute fix-ID_press group-ID pressure fix-ID_temp + + +compute fix-ID_temp all temp +compute fix-ID_press all pressure fix-ID_temp + + See the compute temp and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”. The group for @@ -266,8 +266,10 @@ by including their suffix, or you can use the suffix command in your input script. See Section_accelerate of the manual for more instructions on how to use the accelerated styles effectively. + -Restart, fix_modify, output, run start/stop, minimize info: + +Restart, fix_modify, output, run start/stop, minimize info This fix writes the values of E0, V0, and P0, as well as the state of all the thermostat and barostat variables to binary restart files. See the @@ -291,7 +293,7 @@ compute temperature on a subset of atoms. The fix_modify energy option is supported by these fixes to add the energy change induced by Nose/Hoover thermostatting and barostatting to the system’s potential energy as part of -thermodynamic output. Either way, this energy is *not* +thermodynamic output. Either way, this energy is not included in the definition of internal energy E when calculating the value of Delta in the above equation. These fixes compute a global scalar and a global vector of quantities, diff --git a/doc/html/fix_orient.html b/doc/html/fix_orient.html index 9b01605d28..74dd4d3477 100644 --- a/doc/html/fix_orient.html +++ b/doc/html/fix_orient.html @@ -232,7 +232,9 @@ symmetry, so the list must include one from each pair of equal-and-opposite neighbors. A pair of orientation files for a Sigma=5 tilt boundary are shown below. A tutorial that can help for writing the orientation files is given in (Wicaksono2) -Restart, fix_modify, output, run start/stop, minimize info: + + +Restart, fix_modify, output, run start/stop, minimize info No information about this fix is written to binary restart files. The fix_modify energy option is supported by this fix to add the potential energy of atom interactions with the grain diff --git a/doc/html/fix_pimd.html b/doc/html/fix_pimd.html index 545be26b57..57ee90e294 100644 --- a/doc/html/fix_pimd.html +++ b/doc/html/fix_pimd.html @@ -232,9 +232,9 @@ ring. To run a PIMD simulation with M quasi-beads in each ring polymer using N MPI tasks for each partition’s domain-decomposition, you would use P = MxN processors (cores) and run the simulation as follows: - -mpirun -np P lmp_mpi -partition MxN -in script - +mpirun -np P lmp_mpi -partition MxN -in script + + Note that in the LAMMPS input script for a multi-partition simulation, it is often very useful to define a uloop-style variable such as variable ibead uloop M pad @@ -243,11 +243,11 @@ it is often very useful to define a -dump dcd all dcd 10 system_${ibead}.dcd +dump dcd all dcd 10 system_${ibead}.dcd restart 1000 system_${ibead}.restart1 system_${ibead}.restart2 read_restart system_${ibead}.restart2 - + + Restrictions diff --git a/doc/html/fix_qbmsst.html b/doc/html/fix_qbmsst.html index f3dca0ee47..1fb67f4518 100644 --- a/doc/html/fix_qbmsst.html +++ b/doc/html/fix_qbmsst.html @@ -157,10 +157,10 @@ Examples - -fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units) -fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units) - +fix 1 all qbmsst z 0.122 q 25 mu 0.9 tscale 0.01 damp 200 seed 35082 f_max 0.3 N_f 100 eta 1 beta 400 T_init 110 (liquid methane modeled with the REAX force field, real units) +fix 2 all qbmsst z 72 q 40 tscale 0.05 damp 1 seed 47508 f_max 120.0 N_f 100 eta 1.0 beta 500 T_init 300 (quartz modeled with the BKS force field, metal units) + + Two example input scripts are given, including shocked alpha quartz and shocked liquid methane. The input script first equilibrate an initial state with the quantum thermal bath at the target temperature @@ -242,8 +242,10 @@ thermal bath and the system before shock loading. For all pressure styles, the simulation box stays orthorhombic in shape. Parrinello-Rahman boundary conditions (tilted box) are supported by LAMMPS, but are not implemented for QBMSST. + -Restart, fix_modify, output, run start/stop, minimize info: + +Restart, fix_modify, output, run start/stop, minimize info Because the state of the random number generator is not written to binary restart files, this fix cannot be restarted “exactly” in an uninterrupted fashion. However, in a statistical @@ -269,16 +271,16 @@ headers, the following LAMMPS commands are suggested. Here the fix_modify energy command is also enabled to allow the thermo keyword etotal to print the quantity <i>etot</i>. See also the thermo_style command. - -fix fix_id all msst z -fix_modify fix_id energy yes -variable dhug equal f_fix_id[1] -variable dray equal f_fix_id[2] -variable lgr_vel equal f_fix_id[3] -variable lgr_pos equal f_fix_id[4] -variable T_qm equal f_fix_id[5] -thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id - +fix fix_id all msst z +fix_modify fix_id energy yes +variable dhug equal f_fix_id[1] +variable dray equal f_fix_id[2] +variable lgr_vel equal f_fix_id[3] +variable lgr_pos equal f_fix_id[4] +variable T_qm equal f_fix_id[5] +thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos v_T_qm f_fix_id + + The global scalar under the entry f_fix_id is the quantity of thermo energy as an extra part of <i>etot</i>. This global scalar and the vector of 5 quantities can be accessed by various output commands. It is worth noting that the diff --git a/doc/html/fix_restrain.html b/doc/html/fix_restrain.html index ef8c9949c2..3612f2e3fd 100644 --- a/doc/html/fix_restrain.html +++ b/doc/html/fix_restrain.html @@ -165,15 +165,27 @@ fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 Description Restrain the motion of the specified sets of atoms by making them part of a bond or angle or dihedral interaction whose strength can vary -over time during a simulation. This is functionally equivalent to +over time during a simulation. This is functionally similar to creating a bond or angle or dihedral for the same atoms in a data file, as specified by the read_data command, albeit -with a time-varying pre-factor coefficient. For the purpose of -forcefield parameter-fitting or mapping a molecular potential energy -surface, this fix reduces the hassle and risk associated with -modifying data files. In other words, use this fix to temporarily -force a molecule to adopt a particular conformation. To create a -permanent bond or angle or dihedral, you should modify the data file. +with a time-varying pre-factor coefficient, and except for exclusion +rules, as explained below. +For the purpose of forcefield parameter-fitting or mapping a molecular +potential energy surface, this fix reduces the hassle and risk +associated with modifying data files. In other words, use this fix to +temporarily force a molecule to adopt a particular conformation. To +create a permanent bond or angle or dihedral, you should modify the +data file. + +Note +Adding a bond/angle/dihedral with this command does not apply +the exclusion rules and weighting factors specified by the +special_bonds command to atoms in the restraint +that are now bonded (1-2,1-3,1-4 neighbors) as a result. If they are +close enough to interact in a pair_style sense +(non-bonded interaction), then the bond/angle/dihedral restraint +interaction will simply be superposed on top of that interaction. + The group-ID specified by this fix is ignored. The second example above applies a restraint to hold the dihedral angle formed by atoms 1, 2, 3, and 4 near 120 degrees using a constant diff --git a/doc/html/fix_rx.html b/doc/html/fix_rx.html index 6d337133f8..b39fe17f46 100644 --- a/doc/html/fix_rx.html +++ b/doc/html/fix_rx.html @@ -147,13 +147,13 @@ Examples - -fix 1 all rx kinetics.rx none dense lammps_rk4 -fix 1 all rx kinetics.rx none sparse lammps_rk4 1 -fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10 -fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1 - +fix 1 all rx kinetics.rx none dense lammps_rk4 +fix 1 all rx kinetics.rx none sparse lammps_rk4 1 +fix 1 all rx kinetics.rx lucy sparse lammps_rk4 10 +fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 +fix 1 all rx kinetics.rx none dense rkf45 1 100 1e-6 1e-8 -1 + + Description @@ -271,7 +271,7 @@ temperature exponent n, and the activation energy Ea. are used by the fix eos/table/rx command to define the thermodynamic properties of each species. Furthermore, the number of species molecules (i.e., concentration) can be specified -either with the set command using the “d_” prefix or by +either with the set command using the “d_” prefix or by reading directly the concentrations from a data file. For the latter case, the read_data command with the fix keyword should be specified, where the fix-ID will be the “fix rx`ID with a <SPECIES”>`_ suffix, e.g. diff --git a/doc/html/fix_shake.html b/doc/html/fix_shake.html index 6c279062d0..7cfb03e019 100644 --- a/doc/html/fix_shake.html +++ b/doc/html/fix_shake.html @@ -289,8 +289,10 @@ the RATTLE constraints. You can check whether the constraints work correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp to 1 and recompiling LAMMPS. + -Restart, fix_modify, output, run start/stop, minimize info: + +Restart, fix_modify, output, run start/stop, minimize info No information about these fixes is written to binary restart files. None of the fix_modify options are relevant to these fixes. No global or per-atom quantities are stored by these fixes for access by various output commands. No parameter of these fixes diff --git a/doc/html/fix_spring_rg.html b/doc/html/fix_spring_rg.html index 8cb641326c..aeaa3bece4 100644 --- a/doc/html/fix_spring_rg.html +++ b/doc/html/fix_spring_rg.html @@ -166,7 +166,9 @@ the mass of the entire group. Note that K is thus a force constant for the aggregate force on the group of atoms, not a per-atom force. If RG0 is specified as NULL, then the RG of the group is computed at the time the fix is specified, and that value is used as the target. -Restart, fix_modify, output, run start/stop, minimize info: + + +Restart, fix_modify, output, run start/stop, minimize info No information about this fix is written to binary restart files. None of the fix_modify options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various output commands. No parameter of this fix can diff --git a/doc/html/fix_ti_rs.html b/doc/html/fix_ti_rs.html index f298fc952d..311cabb702 100644 --- a/doc/html/fix_ti_rs.html +++ b/doc/html/fix_ti_rs.html @@ -128,9 +128,9 @@ fix ti/rs command Syntax - -fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ... - +fix ID group-ID ti/rs lambda_initial lambda_final t_switch t_equil keyword value ... + + ID, group-ID are documented in fix command ti/rs = style name of this fix command @@ -198,7 +198,9 @@ scaling is faster at temperatures closer to the initial temperature of the procedure. An example script using this command is provided in the examples/USER/misc/ti directory. -Restart, fix_modify, output, run start/stop, minimize info: + + +Restart, fix_modify, output, run start/stop, minimize info No information about this fix is written to binary restart files. This fix computes a global vector quantitie which can be accessed by various output commands. The vector has diff --git a/doc/html/fix_ti_spring.html b/doc/html/fix_ti_spring.html index e7d63d947a..a0a3a6db23 100644 --- a/doc/html/fix_ti_spring.html +++ b/doc/html/fix_ti_spring.html @@ -128,9 +128,9 @@ fix ti/spring command Syntax - -fix ID group-ID ti/spring K t_switch t_equil keyword value ... - +fix ID group-ID ti/spring K t_switch t_equil keyword value ... + + ID, group-ID are documented in fix command ti/spring = style name of this fix command @@ -205,7 +205,9 @@ issues with the canonical sampling of harmonic degrees of freedom (notice that the chain option will NOT solve this problem). The Langevin thermostat (fix langevin) works fine. -Restart, fix_modify, output, run start/stop, minimize info: + + +Restart, fix_modify, output, run start/stop, minimize info This fix writes the original coordinates of tethered atoms to binary restart files, so that the spring effect will be the same in a restarted simulation. See the read restart command for info on how to re-specify a fix in an input script that reads a restart file, so that the operation of diff --git a/doc/html/fix_ttm.html b/doc/html/fix_ttm.html index 1b12323895..af630d2964 100644 --- a/doc/html/fix_ttm.html +++ b/doc/html/fix_ttm.html @@ -131,50 +131,50 @@ fix ttm/mod command Syntax - -fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile -fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile - +fix ID group-ID ttm seed C_e rho_e kappa_e gamma_p gamma_s v_0 Nx Ny Nz T_infile N T_outfile +fix ID group-ID ttm/mod seed init_file Nx Ny Nz T_infile N T_outfile + + ID, group-ID are documented in fix command style = ttm or ttm_mod seed = random number seed to use for white noise (positive integer) remaining arguments for fix ttm: - -C_e = electronic specific heat (energy/(electron*temperature) units) -rho_e = electronic density (electrons/volume units) -kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units) -gamma_p = friction coefficient due to electron-ion interactions (mass/time units) -gamma_s = friction coefficient due to electronic stopping (mass/time units) -v_0 = electronic stopping critical velocity (velocity units) -Nx = number of thermal solve grid points in the x-direction (positive integer) -Ny = number of thermal solve grid points in the y-direction (positive integer) -Nz = number of thermal solve grid points in the z-direction (positive integer) -T_infile = filename to read initial electronic temperature from -N = dump TTM temperatures every this many timesteps, 0 = no dump -T_outfile = filename to write TTM temperatures to (only needed if N > 0) - +C_e = electronic specific heat (energy/(electron*temperature) units) +rho_e = electronic density (electrons/volume units) +kappa_e = electronic thermal conductivity (energy/(time*distance*temperature) units) +gamma_p = friction coefficient due to electron-ion interactions (mass/time units) +gamma_s = friction coefficient due to electronic stopping (mass/time units) +v_0 = electronic stopping critical velocity (velocity units) +Nx = number of thermal solve grid points in the x-direction (positive integer) +Ny = number of thermal solve grid points in the y-direction (positive integer) +Nz = number of thermal solve grid points in the z-direction (positive integer) +T_infile = filename to read initial electronic temperature from +N = dump TTM temperatures every this many timesteps, 0 = no dump +T_outfile = filename to write TTM temperatures to (only needed if N > 0) + + remaining arguments for fix ttm/mod: - -init_file = file with the parameters to TTM -Nx = number of thermal solve grid points in the x-direction (positive integer) -Ny = number of thermal solve grid points in the y-direction (positive integer) -Nz = number of thermal solve grid points in the z-direction (positive integer) -T_infile = filename to read initial electronic temperature from -N = dump TTM temperatures every this many timesteps, 0 = no dump -T_outfile = filename to write TTM temperatures to (only needed if N > 0) - +init_file = file with the parameters to TTM +Nx = number of thermal solve grid points in the x-direction (positive integer) +Ny = number of thermal solve grid points in the y-direction (positive integer) +Nz = number of thermal solve grid points in the z-direction (positive integer) +T_infile = filename to read initial electronic temperature from +N = dump TTM temperatures every this many timesteps, 0 = no dump +T_outfile = filename to write TTM temperatures to (only needed if N > 0) + + Examples - -fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out -fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out -fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out - +fix 2 all ttm 699489 1.0 1.0 10 0.1 0.0 2.0 1 12 1 initialTs 1000 T.out +fix 2 all ttm 123456 1.0 1.0 1.0 1.0 1.0 5.0 5 5 5 Te.in 1 Te.out +fix 2 all ttm/mod 34277 parameters.txt 5 5 5 T_init 10 T_out + + Description @@ -330,32 +330,34 @@ is calculated as The fix ttm/mod parameter file init_file has the following syntax/ Every line with the odd number is considered as a comment and ignored. The lines with the even numbers are treated as follows: - -a_0, energy/(temperature*electron) units -a_1, energy/(temperature^2*electron) units -a_2, energy/(temperature^3*electron) units -a_3, energy/(temperature^4*electron) units -a_4, energy/(temperature^5*electron) units -C_0, energy/(temperature*electron) units -A, 1/temperature units -rho_e, electrons/volume units -D_e, length^2/time units -gamma_p, mass/time units -gamma_s, mass/time units -v_0, length/time units -I_0, energy/(time*length^2) units -lsurface, electron grid units (positive integer) -rsurface, electron grid units (positive integer) -l_skin, length units -tau, time units -B, dimensionless -lambda, length units -n_ion, ions/volume units -surface_movement: 0 to disable tracking of surface motion, 1 to enable -T_e_min, temperature units - +a_0, energy/(temperature*electron) units +a_1, energy/(temperature^2*electron) units +a_2, energy/(temperature^3*electron) units +a_3, energy/(temperature^4*electron) units +a_4, energy/(temperature^5*electron) units +C_0, energy/(temperature*electron) units +A, 1/temperature units +rho_e, electrons/volume units +D_e, length^2/time units +gamma_p, mass/time units +gamma_s, mass/time units +v_0, length/time units +I_0, energy/(time*length^2) units +lsurface, electron grid units (positive integer) +rsurface, electron grid units (positive integer) +l_skin, length units +tau, time units +B, dimensionless +lambda, length units +n_ion, ions/volume units +surface_movement: 0 to disable tracking of surface motion, 1 to enable +T_e_min, temperature units + + + -Restart, fix_modify, output, run start/stop, minimize info: + +Restart, fix_modify, output, run start/stop, minimize info These fixes write the state of the electronic subsystem and the energy exchange between the subsystems to binary restart files. See the read_restart command for info on how to re-specify a fix in an input script that reads a diff --git a/doc/html/fix_wall.html b/doc/html/fix_wall.html index 0a1d123b92..8f3ac46551 100644 --- a/doc/html/fix_wall.html +++ b/doc/html/fix_wall.html @@ -179,12 +179,12 @@ args = coord epsilon sigma cutoff Examples - -fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box -fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5 -fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5 -fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 - +fix wallhi all wall/lj93 xlo -1.0 1.0 1.0 2.5 units box +fix wallhi all wall/lj93 xhi EDGE 1.0 1.0 2.5 +fix wallhi all wall/lj126 v_wiggle 23.2 1.0 1.0 2.5 +fix zwalls all wall/colloid zlo 0.0 1.0 1.0 0.858 zhi 40.0 1.0 1.0 0.858 + + Description @@ -321,22 +321,22 @@ want. in a time-dependent fashion using equal-style variables. The wall interaction parameters (epsilon, sigma) could be varied with additional variable definitions. - -variable ramp equal ramp(0,10) -fix 1 all wall xlo v_ramp 1.0 1.0 2.5 - - -variable linear equal vdisplace(0,20) -fix 1 all wall xlo v_linear 1.0 1.0 2.5 - - -variable wiggle equal swiggle(0.0,5.0,3.0) -fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 - - -variable wiggle equal cwiggle(0.0,5.0,3.0) -fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 - +variable ramp equal ramp(0,10) +fix 1 all wall xlo v_ramp 1.0 1.0 2.5 + + +variable linear equal vdisplace(0,20) +fix 1 all wall xlo v_linear 1.0 1.0 2.5 + + +variable wiggle equal swiggle(0.0,5.0,3.0) +fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 + + +variable wiggle equal cwiggle(0.0,5.0,3.0) +fix 1 all wall xlo v_wiggle 1.0 1.0 2.5 + + The ramp(lo,hi) function adjusts the wall position linearly from lo to hi over the course of a run. The vdisplace(c0,velocity) function does something similar using the equation position = c0 + velocity*delta, @@ -344,18 +344,20 @@ where delta is the elapsed time. The swiggle(c0,A,period) function causes the wall position to oscillate sinusoidally according to this equation, where omega = 2 PI / period: - -position = c0 + A sin(omega*delta) - +position = c0 + A sin(omega*delta) + + The cwiggle(c0,A,period) function causes the wall position to oscillate sinusoidally according to this equation, which will have an initial wall velocity of 0.0, and thus may impose a gentler perturbation on the particles: - -position = c0 + A (1 - cos(omega*delta)) - +position = c0 + A (1 - cos(omega*delta)) + + + -Restart, fix_modify, output, run start/stop, minimize info: + +Restart, fix_modify, output, run start/stop, minimize info No information about this fix is written to binary restart files. The fix_modify energy option is supported by this fix to add the energy of interaction between atoms and each wall to diff --git a/doc/html/fix_wall_region.html b/doc/html/fix_wall_region.html index ba645d66ef..4f24bee99a 100644 --- a/doc/html/fix_wall_region.html +++ b/doc/html/fix_wall_region.html @@ -280,7 +280,9 @@ and does not blow up as r -> 0, but you must use a large enough epsilon that particles always reamin on the correct side of the region surface (r > 0). -Restart, fix_modify, output, run start/stop, minimize info: + + +Restart, fix_modify, output, run start/stop, minimize info No information about this fix is written to binary restart files. The fix_modify energy option is supported by this fix to add the energy of interaction between atoms and the wall to the diff --git a/doc/html/genindex.html b/doc/html/genindex.html index b40e27bf00..0e140ad1a1 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -156,93 +156,93 @@ - angle\_coeff + angle_coeff - angle\_style + angle_style - angle\_style charmm + angle_style charmm - angle\_style class2 + angle_style class2 - angle\_style cosine + angle_style cosine - angle\_style cosine/delta + angle_style cosine/delta - angle\_style cosine/periodic + angle_style cosine/periodic - angle\_style cosine/shift + angle_style cosine/shift - angle\_style cosine/shift/exp + angle_style cosine/shift/exp - angle\_style cosine/squared + angle_style cosine/squared - angle\_style dipole + angle_style dipole - angle\_style fourier + angle_style fourier - angle\_style fourier/simple + angle_style fourier/simple - angle\_style harmonic + angle_style harmonic - angle\_style hybrid + angle_style hybrid - angle\_style none + angle_style none - angle\_style quartic + angle_style quartic - angle\_style sdk + angle_style sdk - angle\_style table + angle_style table - angle\_style zero + angle_style zero - atom\_modify + atom_modify - atom\_style + atom_style @@ -256,69 +256,69 @@ - bond\_coeff + bond_coeff - bond\_style + bond_style - bond\_style class2 + bond_style class2 - bond\_style fene + bond_style fene - bond\_style fene/expand + bond_style fene/expand - bond\_style harmonic + bond_style harmonic - bond\_style harmonic/shift + bond_style harmonic/shift - bond\_style harmonic/shift/cut + bond_style harmonic/shift/cut - bond\_style hybrid + bond_style hybrid - bond\_style morse + bond_style morse - bond\_style none + bond_style none - bond\_style nonlinear + bond_style nonlinear - bond\_style quartic + bond_style quartic - bond\_style table + bond_style table - bond\_style zero + bond_style zero - bond\_write + bond_write @@ -336,7 +336,7 @@ - change\_box + change_box @@ -344,11 +344,11 @@ - comm\_modify + comm_modify - comm\_style + comm_style @@ -798,19 +798,19 @@ - compute\_modify + compute_modify - create\_atoms + create_atoms - create\_bonds + create_bonds - create\_box + create_box @@ -820,11 +820,11 @@ - delete\_atoms + delete_atoms - delete\_bonds + delete_bonds @@ -832,73 +832,73 @@ - dihedral\_coeff - - - - dihedral\_style - - - - dihedral\_style charmm - - - - dihedral\_style class2 - - - - dihedral\_style cosine/shift/exp - - - - dihedral\_style fourier - - - dihedral\_style harmonic - dihedral\_style helix + dihedral_coeff - dihedral\_style hybrid + dihedral_style - dihedral\_style multi/harmonic + dihedral_style charmm - dihedral\_style nharmonic + dihedral_style class2 + + + + dihedral_style cosine/shift/exp + + + + dihedral_style fourier + + + + dihedral_style helix + + + + dihedral_style hybrid + + + + dihedral_style multi/harmonic + + + + dihedral_style nharmonic - dihedral\_style none + dihedral_style none - dihedral\_style opls + dihedral_style opls - dihedral\_style quadratic + dihedral_style quadratic - dihedral\_style spherical + dihedral_style spherical - dihedral\_style table + dihedral_style table - dihedral\_style zero + dihedral_style zero @@ -906,7 +906,7 @@ - displace\_atoms + displace_atoms @@ -930,7 +930,7 @@ - dump\_modify + dump_modify @@ -1408,19 +1408,19 @@ - fix smd/adjust\_dt + fix smd/adjust_dt - fix smd/integrate\_tlsph + fix smd/integrate_tlsph - fix smd/integrate\_ulsph + fix smd/integrate_ulsph - fix smd/move\_tri\_surf + fix smd/move_tri_surf @@ -1428,7 +1428,7 @@ - fix smd/wall\_surface + fix smd/wall_surface @@ -1540,7 +1540,7 @@ - fix\_modify + fix_modify @@ -1570,57 +1570,57 @@ - improper\_coeff + improper_coeff - improper\_style + improper_style - improper\_style class2 + improper_style class2 - improper\_style cossq + improper_style cossq - improper\_style cvff + improper_style cvff - improper\_style distance + improper_style distance - improper\_style fourier + improper_style fourier - improper\_style harmonic + improper_style harmonic - improper\_style hybrid + improper_style hybrid - improper\_style none + improper_style none - improper\_style ring + improper_style ring - improper\_style umbrella + improper_style umbrella - improper\_style zero + improper_style zero @@ -1648,13 +1648,13 @@ - kspace\_modify + kspace_modify - kspace\_style + kspace_style @@ -1688,11 +1688,11 @@ - min\_modify + min_modify - min\_style + min_style @@ -1744,336 +1744,22 @@ - pair\_coeff - - - pair\_modify - pair\_style - - - - pair\_style adp - - - - pair\_style airebo - - - - pair\_style awpmd/cut - - - - pair\_style beck - - - - pair\_style body - - - pair\_style bop - pair\_style born - - - - pair\_style born/coul/long/cs - - - - pair\_style brownian - - - - pair\_style buck - - - pair\_style buck/long/coul/long - pair\_style colloid - - - - pair\_style comb - - - - pair\_style coul/cut - - - - pair\_style coul/diel - - - - pair\_style dpd - - - - pair\_style dpd/fdt - - - - pair\_style dsmc - - - - pair\_style eam - - - - pair\_style edip - - - - pair\_style eff/cut - - - - pair\_style eim - - - - pair\_style exp6/rx - - - - pair\_style gauss - - - - pair\_style gayberne - - - pair\_style gran/hooke - pair\_style hbond/dreiding/lj - - - - pair\_style hybrid - - - - pair\_style kim - - - - pair\_style lcbop - - - - pair\_style line/lj - - - - pair\_style list - - - - pair\_style lj/charmm/coul/charmm - - - - pair\_style lj/class2 - - - - pair\_style lj/cubic - - - - pair\_style lj/cut - - - - pair\_style lj/cut/dipole/cut - - - - pair\_style lj/cut/soft - - - - pair\_style lj/expand - - - - pair\_style lj/gromacs - - - - pair\_style lj/long/coul/long - - - - pair\_style lj/mdf - - - - pair\_style lj/sdk - - - - pair\_style lj/sf - - - - pair\_style lj/smooth - - - - pair\_style lj/smooth/linear - - - - pair\_style lj96/cut - - - - - - pair\_style lubricate - - - - pair\_style lubricateU - - - - pair\_style meam - - - - pair\_style mgpt - - - - pair\_style mie/cut - - - - pair\_style morse - - - - pair\_style multi/lucy - - - - pair\_style multi/lucy/rx - - - - pair\_style nb3b/harmonic - - - - pair\_style nm/cut - - - - pair\_style none - - - - pair\_style peri/pmb - - - - pair\_style polymorphic - - - - pair\_style quip - - - - pair\_style reax - - - - pair\_style reax/c - - - - pair\_style resquared - - - - pair\_style smd/hertz - - - - pair\_style smd/tlsph - - - - pair\_style smd/tri\_surface - - - - pair\_style smd/ulsph - - - - pair\_style smtbq - - - - pair\_style snap - - - - pair\_style soft - - - - pair\_style sph/heatconduction - - - - pair\_style sph/idealgas - - - - pair\_style sph/lj - - - - pair\_style sph/rhosum - - - - pair\_style sph/taitwater - - - - pair\_style sph/taitwater/morris - - - - pair\_style srp - - - - pair\_style sw - - - pair\_style table @@ -2082,47 +1768,361 @@ - pair\_style tersoff + pair_coeff - pair\_style tersoff/mod + pair_style - pair\_style tersoff/zbl + pair_style adp - pair\_style thole + pair_style airebo - pair\_style tri/lj + pair_style awpmd/cut - pair\_style vashishta + pair_style beck - pair\_style yukawa + pair_style body - pair\_style yukawa/colloid + pair_style born - pair\_style zbl + pair_style born/coul/long/cs - pair\_style zero + pair_style brownian - pair\_write + pair_style buck + + + + pair_style colloid + + + + pair_style comb + + + + pair_style coul/cut + + + + pair_style coul/diel + + + + pair_style dpd + + + + pair_style dpd/fdt + + + + pair_style dsmc + + + + pair_style eam + + + + pair_style edip + + + + pair_style eff/cut + + + + pair_style eim + + + + pair_style exp6/rx + + + + pair_style gauss + + + + pair_style gayberne + + + + pair_style hbond/dreiding/lj + + + + pair_style hybrid + + + + pair_style kim + + + + pair_style lcbop + + + + pair_style line/lj + + + + pair_style list + + + + pair_style lj/charmm/coul/charmm + + + + pair_style lj/class2 + + + + pair_style lj/cubic + + + + pair_style lj/cut + + + + pair_style lj/cut/dipole/cut + + + + pair_style lj/cut/soft + + + + pair_style lj/expand + + + + pair_style lj/gromacs + + + + pair_style lj/long/coul/long + + + + pair_style lj/mdf + + + + pair_style lj/sdk + + + + pair_style lj/sf + + + + pair_style lj/smooth + + + + + + pair_style lj/smooth/linear + + + + pair_style lj96/cut + + + + pair_style lubricate + + + + pair_style lubricateU + + + + pair_style meam + + + + pair_style mgpt + + + + pair_style mie/cut + + + + pair_style morse + + + + pair_style multi/lucy + + + + pair_style multi/lucy/rx + + + + pair_style nb3b/harmonic + + + + pair_style nm/cut + + + + pair_style none + + + + pair_style peri/pmb + + + + pair_style polymorphic + + + + pair_style quip + + + + pair_style reax + + + + pair_style reax/c + + + + pair_style resquared + + + + pair_style smd/hertz + + + + pair_style smd/tlsph + + + + pair_style smd/tri_surface + + + + pair_style smd/ulsph + + + + pair_style smtbq + + + + pair_style snap + + + + pair_style soft + + + + pair_style sph/heatconduction + + + + pair_style sph/idealgas + + + + pair_style sph/lj + + + + pair_style sph/rhosum + + + + pair_style sph/taitwater + + + + pair_style sph/taitwater/morris + + + + pair_style srp + + + + pair_style sw + + + + pair_style tersoff + + + + pair_style tersoff/mod + + + + pair_style tersoff/zbl + + + + pair_style thole + + + + pair_style tri/lj + + + + pair_style vashishta + + + + pair_style yukawa + + + + pair_style yukawa/colloid + + + + pair_style zbl + + + + pair_style zero + + + + pair_write @@ -2166,11 +2166,11 @@ - read\_dump + read_dump - read\_restart + read_restart @@ -2188,7 +2188,7 @@ - reset\_timestep + reset_timestep @@ -2200,7 +2200,7 @@ - run\_style + run_style @@ -2220,7 +2220,7 @@ - special\_bonds + special_bonds @@ -2246,13 +2246,13 @@ - thermo\_modify + thermo_modify - thermo\_style + thermo_style @@ -2310,21 +2310,21 @@ - write\_coeff + write\_dump - write\_data + write_coeff - write\_dump + write_data - write\_restart + write_restart diff --git a/doc/html/improper_class2.html b/doc/html/improper_class2.html index 0d39e5935a..c6758cff97 100644 --- a/doc/html/improper_class2.html +++ b/doc/html/improper_class2.html @@ -131,17 +131,17 @@ improper_style class2/omp command Syntax - -improper_style class2 - +improper_style class2 + + Examples - -improper_style class2 -improper_coeff 1 100.0 0 -improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06 - +improper_style class2 +improper_coeff 1 100.0 0 +improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06 + + Description diff --git a/doc/html/improper_cossq.html b/doc/html/improper_cossq.html index 28c2370f09..9a7aa85c8d 100644 --- a/doc/html/improper_cossq.html +++ b/doc/html/improper_cossq.html @@ -131,16 +131,16 @@ improper_style cossq/omp command Syntax - -improper_style cossq - +improper_style cossq + + Examples - -improper_style cossq -improper_coeff 1 4.0 0.0 - +improper_style cossq +improper_coeff 1 4.0 0.0 + + Description diff --git a/doc/html/improper_cvff.html b/doc/html/improper_cvff.html index 461f02eeab..186c5aa3e1 100644 --- a/doc/html/improper_cvff.html +++ b/doc/html/improper_cvff.html @@ -134,16 +134,16 @@ improper_style cvff/omp command Syntax - -improper_style cvff - +improper_style cvff + + Examples - -improper_style cvff -improper_coeff 1 80.0 -1 4 - +improper_style cvff +improper_coeff 1 80.0 -1 4 + + Description diff --git a/doc/html/improper_distance.html b/doc/html/improper_distance.html index 3f42cef8d0..69718ece9a 100644 --- a/doc/html/improper_distance.html +++ b/doc/html/improper_distance.html @@ -132,10 +132,10 @@ Examples - -improper_style distance -improper_coeff 1 80.0 100.0 - +improper_style distance +improper_coeff 1 80.0 100.0 + + Description diff --git a/doc/html/improper_fourier.html b/doc/html/improper_fourier.html index be22144ccf..545282aa2a 100644 --- a/doc/html/improper_fourier.html +++ b/doc/html/improper_fourier.html @@ -131,16 +131,16 @@ improper_style fourier/omp command Syntax - -improper_style fourier - +improper_style fourier + + Examples - -improper_style fourier -improper_coeff 1 100.0 180.0 - +improper_style fourier +improper_coeff 1 100.0 180.0 + + Description diff --git a/doc/html/improper_harmonic.html b/doc/html/improper_harmonic.html index 11553c0187..d268c62014 100644 --- a/doc/html/improper_harmonic.html +++ b/doc/html/improper_harmonic.html @@ -137,16 +137,16 @@ improper_style harmonic/omp command Syntax - -improper_style harmonic - +improper_style harmonic + + Examples - -improper_style harmonic -improper_coeff 1 100.0 0 - +improper_style harmonic +improper_coeff 1 100.0 0 + + Description diff --git a/doc/html/improper_ring.html b/doc/html/improper_ring.html index 0e7e4330b0..aa3b557a57 100644 --- a/doc/html/improper_ring.html +++ b/doc/html/improper_ring.html @@ -131,16 +131,16 @@ improper_style ring/omp command Syntax - -improper_style ring - +improper_style ring + + Examples - -improper_style ring -improper_coeff 1 8000 70.5 - +improper_style ring +improper_coeff 1 8000 70.5 + + Description @@ -150,8 +150,8 @@ improper_coeff 1 8000 70.5 specified by (i,j,k,l) indices and theta0 its equilibrium value. If the 4 atoms in an improper quadruplet (listed in the data file read by the read_data command) are ordered i,j,k,l then -theta_ijl is the angle between atoms i,j and l, theta_ijk is the -angle between atoms i,j and k, theta_kjl is the angle between atoms +theta_ijl is the angle between atoms i,j and l, theta_ijk is the +angle between atoms i,j and k, theta_kjl is the angle between atoms j,k, and l. The “ring” improper style implements the improper potential introduced by Destree et al., in Equation (9) of (Destree). This diff --git a/doc/html/improper_umbrella.html b/doc/html/improper_umbrella.html index de79db67ef..f1fb943d5e 100644 --- a/doc/html/improper_umbrella.html +++ b/doc/html/improper_umbrella.html @@ -131,16 +131,16 @@ improper_style umbrella/omp command Syntax - -improper_style umbrella - +improper_style umbrella + + Examples - -improper_style umbrella -improper_coeff 1 100.0 180.0 - +improper_style umbrella +improper_coeff 1 100.0 180.0 + + Description diff --git a/doc/html/pair_adp.html b/doc/html/pair_adp.html index 5bc88ab7d0..c38bbab6b5 100644 --- a/doc/html/pair_adp.html +++ b/doc/html/pair_adp.html @@ -131,17 +131,17 @@ pair_style adp/omp command Syntax - -pair_style adp - +pair_style adp + + Examples - -pair_style adp -pair_coeff * * Ta.adp Ta -pair_coeff * * ../potentials/AlCu.adp Al Al Cu - +pair_style adp +pair_coeff * * Ta.adp Ta +pair_coeff * * ../potentials/AlCu.adp Al Al Cu + + Description @@ -188,9 +188,9 @@ file which has tabulated ADP values for w elements and their alloy interactions: Cu and Al. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Al, and the 4th to be Cu, you would use the following pair_coeff command: - -pair_coeff * * AlCu.adp Al Al Al Cu - +pair_coeff * * AlCu.adp Al Al Al Cu + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Al arguments map LAMMPS atom types 1,2,3 to the Al element in the extended setfl file. The final Cu argument maps diff --git a/doc/html/pair_airebo.html b/doc/html/pair_airebo.html index 6827568073..503da5ef6a 100644 --- a/doc/html/pair_airebo.html +++ b/doc/html/pair_airebo.html @@ -143,9 +143,9 @@ pair_style rebo/omp command Syntax - -pair_style style cutoff LJ_flag TORSION_flag - +pair_style style cutoff LJ_flag TORSION_flag + + style = airebo or airebo/morse or rebo cutoff = LJ or Morse cutoff (sigma scale factor) (AIREBO and AIREBO-M only) @@ -155,19 +155,19 @@ pair_style style cutoff LJ_flag TORSION_flag Examples - -pair_style airebo 3.0 -pair_style airebo 2.5 1 0 -pair_coeff * * ../potentials/CH.airebo H C - - -pair_style airebo/morse 3.0 -pair_coeff * * ../potentials/CH.airebo-m H C - - -pair_style rebo -pair_coeff * * ../potentials/CH.airebo H C - +pair_style airebo 3.0 +pair_style airebo 2.5 1 0 +pair_coeff * * ../potentials/CH.airebo H C + + +pair_style airebo/morse 3.0 +pair_coeff * * ../potentials/CH.airebo-m H C + + +pair_style rebo +pair_coeff * * ../potentials/CH.airebo H C + + Description @@ -242,9 +242,9 @@ to specify the path for the potential file. As an example, if your LAMMPS simulation has 4 atom types and you want the 1st 3 to be C, and the 4th to be H, you would use the following pair_coeff command: - -pair_coeff * * CH.airebo C C C H - +pair_coeff * * CH.airebo C C C H + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three C arguments map LAMMPS atom types 1,2,3 to the C element in the AIREBO file. The final H argument maps LAMMPS atom @@ -273,13 +273,13 @@ The 3 values correspond to the following sub-categories: To print these quantities to the log file (with descriptive column headings) the following commands could be included in an input script: - -compute 0 all pair airebo -variable REBO equal c_0[1] -variable LJ equal c_0[2] -variable TORSION equal c_0[3] -thermo_style custom step temp epair v_REBO v_LJ v_TORSION - +compute 0 all pair airebo +variable REBO equal c_0[1] +variable LJ equal c_0[2] +variable TORSION equal c_0[3] +thermo_style custom step temp epair v_REBO v_LJ v_TORSION + + Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. diff --git a/doc/html/pair_beck.html b/doc/html/pair_beck.html index baf69eecfa..10325668e8 100644 --- a/doc/html/pair_beck.html +++ b/doc/html/pair_beck.html @@ -134,20 +134,20 @@ pair_style beck/omp command Syntax - -pair_style beck Rc - +pair_style beck Rc + + Rc = cutoff for interactions (distance units) Examples - -pair_style beck 8.0 -pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 -pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0 - +pair_style beck 8.0 +pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 +pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0 + + Description diff --git a/doc/html/pair_body.html b/doc/html/pair_body.html index 5f623fb0b7..5f4df83aa4 100644 --- a/doc/html/pair_body.html +++ b/doc/html/pair_body.html @@ -128,18 +128,18 @@ pair_style body command Syntax - -pair_style body cutoff - +pair_style body cutoff + + cutoff = global cutoff for interactions (distance units) Examples - -pair_style body 3.0 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.5 2.5 - +pair_style body 3.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.0 1.5 2.5 + + Description diff --git a/doc/html/pair_born.html b/doc/html/pair_born.html index c73ca9761f..3740bb4699 100644 --- a/doc/html/pair_born.html +++ b/doc/html/pair_born.html @@ -161,9 +161,9 @@ pair_style born/coul/wolf/omp command Syntax - -pair_style style args - +pair_style style args + + style = born or born/coul/long or born/coul/long/cs or born/coul/msm or born/coul/wolf args = list of arguments for a particular style @@ -185,31 +185,31 @@ pair_style style args Examples - -pair_style born 10.0 -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 - - -pair_style born/coul/long 10.0 -pair_style born/coul/long/cs 10.0 -pair_style born/coul/long 10.0 8.0 -pair_style born/coul/long/cs 10.0 8.0 -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 - - -pair_style born/coul/msm 10.0 -pair_style born/coul/msm 10.0 8.0 -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 - - -pair_style born/coul/wolf 0.25 10.0 -pair_style born/coul/wolf 0.25 10.0 9.0 -pair_coeff * * 6.08 0.317 2.340 24.18 11.51 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 - +pair_style born 10.0 +pair_coeff * * 6.08 0.317 2.340 24.18 11.51 +pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 + + +pair_style born/coul/long 10.0 +pair_style born/coul/long/cs 10.0 +pair_style born/coul/long 10.0 8.0 +pair_style born/coul/long/cs 10.0 8.0 +pair_coeff * * 6.08 0.317 2.340 24.18 11.51 +pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 + + +pair_style born/coul/msm 10.0 +pair_style born/coul/msm 10.0 8.0 +pair_coeff * * 6.08 0.317 2.340 24.18 11.51 +pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 + + +pair_style born/coul/wolf 0.25 10.0 +pair_style born/coul/wolf 0.25 10.0 9.0 +pair_coeff * * 6.08 0.317 2.340 24.18 11.51 +pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 + + Description diff --git a/doc/html/pair_buck.html b/doc/html/pair_buck.html index fa537931bf..58eccb8ce8 100644 --- a/doc/html/pair_buck.html +++ b/doc/html/pair_buck.html @@ -179,9 +179,9 @@ pair_style buck/coul/msm/omp command Syntax - -pair_style style args - +pair_style style args + + style = buck or buck/coul/cut or buck/coul/long or buck/coul/long/cs or buck/coul/msm args = list of arguments for a particular style @@ -202,32 +202,32 @@ pair_style style args Examples - -pair_style buck 2.5 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff * * 100.0 1.5 200.0 3.0 - - -pair_style buck/coul/cut 10.0 -pair_style buck/coul/cut 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 - - -pair_style buck/coul/long 10.0 -pair_style buck/coul/long/cs 10.0 -pair_style buck/coul/long 10.0 8.0 -pair_style buck/coul/long/cs 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 - - -pair_style buck/coul/msm 10.0 -pair_style buck/coul/msm 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 - +pair_style buck 2.5 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff * * 100.0 1.5 200.0 3.0 + + +pair_style buck/coul/cut 10.0 +pair_style buck/coul/cut 10.0 8.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff 1 1 100.0 1.5 200.0 9.0 +pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 + + +pair_style buck/coul/long 10.0 +pair_style buck/coul/long/cs 10.0 +pair_style buck/coul/long 10.0 8.0 +pair_style buck/coul/long/cs 10.0 8.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff 1 1 100.0 1.5 200.0 9.0 + + +pair_style buck/coul/msm 10.0 +pair_style buck/coul/msm 10.0 8.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff 1 1 100.0 1.5 200.0 9.0 + + Description diff --git a/doc/html/pair_charmm.html b/doc/html/pair_charmm.html index 93e44709ce..75994eddd2 100644 --- a/doc/html/pair_charmm.html +++ b/doc/html/pair_charmm.html @@ -158,9 +158,9 @@ pair_style lj/charmm/coul/msm/omp command Syntax - -pair_style style args - +pair_style style args + + style = lj/charmm/coul/charmm or lj/charmm/coul/charmm/implicit or lj/charmm/coul/long or lj/charmm/coul/msm args = list of arguments for a particular style @@ -182,30 +182,30 @@ pair_style style args Examples - -pair_style lj/charmm/coul/charmm 8.0 10.0 -pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 - - -pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 -pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 - - -pair_style lj/charmm/coul/long 8.0 10.0 -pair_style lj/charmm/coul/long 8.0 10.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 - - -pair_style lj/charmm/coul/msm 8.0 10.0 -pair_style lj/charmm/coul/msm 8.0 10.0 9.0 -pair_coeff * * 100.0 2.0 -pair_coeff 1 1 100.0 2.0 150.0 3.5 - +pair_style lj/charmm/coul/charmm 8.0 10.0 +pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0 +pair_coeff * * 100.0 2.0 +pair_coeff 1 1 100.0 2.0 150.0 3.5 + + +pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 +pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0 +pair_coeff * * 100.0 2.0 +pair_coeff 1 1 100.0 2.0 150.0 3.5 + + +pair_style lj/charmm/coul/long 8.0 10.0 +pair_style lj/charmm/coul/long 8.0 10.0 9.0 +pair_coeff * * 100.0 2.0 +pair_coeff 1 1 100.0 2.0 150.0 3.5 + + +pair_style lj/charmm/coul/msm 8.0 10.0 +pair_style lj/charmm/coul/msm 8.0 10.0 9.0 +pair_coeff * * 100.0 2.0 +pair_coeff 1 1 100.0 2.0 150.0 3.5 + + Description diff --git a/doc/html/pair_class2.html b/doc/html/pair_class2.html index a2dee8a442..5e62dd99ef 100644 --- a/doc/html/pair_class2.html +++ b/doc/html/pair_class2.html @@ -158,9 +158,9 @@ pair_style lj/class2/coul/long/omp command Syntax - -pair_style style args - +pair_style style args + + style = lj/class2 or lj/class2/coul/cut or lj/class2/coul/long args = list of arguments for a particular style @@ -178,24 +178,24 @@ pair_style style args Examples - -pair_style lj/class2 10.0 -pair_coeff * * 100.0 2.5 -pair_coeff 1 2* 100.0 2.5 9.0 - - -pair_style lj/class2/coul/cut 10.0 -pair_style lj/class2/coul/cut 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 -pair_coeff 1 1 100.0 3.5 9.0 9.0 - - -pair_style lj/class2/coul/long 10.0 -pair_style lj/class2/coul/long 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - +pair_style lj/class2 10.0 +pair_coeff * * 100.0 2.5 +pair_coeff 1 2* 100.0 2.5 9.0 + + +pair_style lj/class2/coul/cut 10.0 +pair_style lj/class2/coul/cut 10.0 8.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 +pair_coeff 1 1 100.0 3.5 9.0 9.0 + + +pair_style lj/class2/coul/long 10.0 +pair_style lj/class2/coul/long 10.0 8.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + + Description diff --git a/doc/html/pair_colloid.html b/doc/html/pair_colloid.html index a1520bc730..c4254f1606 100644 --- a/doc/html/pair_colloid.html +++ b/doc/html/pair_colloid.html @@ -134,22 +134,22 @@ pair_style colloid/omp command Syntax - -pair_style colloid cutoff - +pair_style colloid cutoff + + cutoff = global cutoff for colloidal interactions (distance units) Examples - -pair_style colloid 10.0 -pair_coeff * * 25 1.0 10.0 10.0 -pair_coeff 1 1 144 1.0 0.0 0.0 3.0 -pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0 -pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0 - +pair_style colloid 10.0 +pair_coeff * * 25 1.0 10.0 10.0 +pair_coeff 1 1 144 1.0 0.0 0.0 3.0 +pair_coeff 1 2 75.398 1.0 0.0 10.0 9.0 +pair_coeff 2 2 39.478 1.0 10.0 10.0 25.0 + + Description diff --git a/doc/html/pair_comb.html b/doc/html/pair_comb.html index c0768ee36a..d7ca86f242 100644 --- a/doc/html/pair_comb.html +++ b/doc/html/pair_comb.html @@ -134,10 +134,10 @@ pair_style comb3 command Syntax - -pair_style comb -pair_style comb3 keyword - +pair_style comb +pair_style comb3 keyword + + keyword = polar polar value = polar_on or polar_off = whether or not to include atomic polarization @@ -145,15 +145,15 @@ keyword = polar Examples - -pair_style comb -pair_coeff * * ../potentials/ffield.comb Si -pair_coeff * * ../potentials/ffield.comb Hf Si O - - -pair_style comb3 polar_off -pair_coeff * * ../potentials/ffield.comb3 O Cu N C O - +pair_style comb +pair_coeff * * ../potentials/ffield.comb Si +pair_coeff * * ../potentials/ffield.comb Hf Si O + + +pair_style comb3 polar_off +pair_coeff * * ../potentials/ffield.comb3 O Cu N C O + + Description @@ -191,9 +191,9 @@ command, where N is the number of LAMMPS atom types. HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would use the following pair_coeff command: - -pair_coeff * * ../potentials/ffield.comb Si Hf O Si - +pair_coeff * * ../potentials/ffield.comb Si Hf O Si + + The first two arguments must be * * so as to span all LAMMPS atom types. The first and last Si arguments map LAMMPS atom types 1 and 4 to the Si element in the ffield.comb file. The second Hf argument diff --git a/doc/html/pair_coul.html b/doc/html/pair_coul.html index 98cba31724..1df9e6791a 100644 --- a/doc/html/pair_coul.html +++ b/doc/html/pair_coul.html @@ -206,18 +206,18 @@ pair_style tip4p/long/omp command Syntax - -pair_style coul/cut cutoff -pair_style coul/debye kappa cutoff -pair_style coul/dsf alpha cutoff -pair_style coul/long cutoff -pair_style coul/long/cs cutoff -pair_style coul/long/gpu cutoff -pair_style coul/wolf alpha cutoff -pair_style coul/streitz cutoff keyword alpha -pair_style tip4p/cut otype htype btype atype qdist cutoff -pair_style tip4p/long otype htype btype atype qdist cutoff - +pair_style coul/cut cutoff +pair_style coul/debye kappa cutoff +pair_style coul/dsf alpha cutoff +pair_style coul/long cutoff +pair_style coul/long/cs cutoff +pair_style coul/long/gpu cutoff +pair_style coul/wolf alpha cutoff +pair_style coul/streitz cutoff keyword alpha +pair_style tip4p/cut otype htype btype atype qdist cutoff +pair_style tip4p/long otype htype btype atype qdist cutoff + + cutoff = global cutoff for Coulombic interactions kappa = Debye length (inverse distance units) @@ -226,46 +226,46 @@ pair_style tip4p/long otype htype btype atype qdist cutoff Examples - -pair_style coul/cut 2.5 -pair_coeff * * -pair_coeff 2 2 3.5 - - -pair_style coul/debye 1.4 3.0 -pair_coeff * * -pair_coeff 2 2 3.5 - - -pair_style coul/dsf 0.05 10.0 -pair_coeff * * - - -pair_style coul/long 10.0 -pair_style coul/long/cs 10.0 -pair_coeff * * - - -pair_style coul/msm 10.0 -pair_coeff * * - - -pair_style coul/wolf 0.2 9.0 -pair_coeff * * - - -pair_style coul/streitz 12.0 ewald -pair_style coul/streitz 12.0 wolf 0.30 -pair_coeff * * AlO.streitz Al O - - -pair_style tip4p/cut 1 2 7 8 0.15 12.0 -pair_coeff * * - - -pair_style tip4p/long 1 2 7 8 0.15 10.0 -pair_coeff * * - +pair_style coul/cut 2.5 +pair_coeff * * +pair_coeff 2 2 3.5 + + +pair_style coul/debye 1.4 3.0 +pair_coeff * * +pair_coeff 2 2 3.5 + + +pair_style coul/dsf 0.05 10.0 +pair_coeff * * + + +pair_style coul/long 10.0 +pair_style coul/long/cs 10.0 +pair_coeff * * + + +pair_style coul/msm 10.0 +pair_coeff * * + + +pair_style coul/wolf 0.2 9.0 +pair_coeff * * + + +pair_style coul/streitz 12.0 ewald +pair_style coul/streitz 12.0 wolf 0.30 +pair_coeff * * AlO.streitz Al O + + +pair_style tip4p/cut 1 2 7 8 0.15 12.0 +pair_coeff * * + + +pair_style tip4p/long 1 2 7 8 0.15 10.0 +pair_coeff * * + + Description @@ -317,21 +317,21 @@ used with p short-range potential that has been parameterized appropriately) via the pair_style hybrid/overlay command. Likewise, charge equilibration must be performed via the fix qeq/slater command. For example: - -pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy -pair_coeff * * coul/streitz AlO.streitz Al O -pair_coeff * * eam/alloy AlO.eam.alloy Al O -fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz - +pair_style hybrid/overlay coul/streitz 12.0 wolf 0.31 eam/alloy +pair_coeff * * coul/streitz AlO.streitz Al O +pair_coeff * * eam/alloy AlO.eam.alloy Al O +fix 1 all qeq/slater 1 12.0 1.0e-6 100 coul/streitz + + The keyword wolf in the coul/streitz command denotes computing Coulombic interactions via Wolf summation. An additional damping parameter is required for the Wolf summation, as described for the coul/wolf potential above. Alternatively, Coulombic interactions can be computed via an Ewald summation. For example: - -pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy -kspace_style ewald 1e-6 - +pair_style hybrid/overlay coul/streitz 12.0 ewald eam/alloy +kspace_style ewald 1e-6 + + Keyword ewald does not need a damping parameter, but a kspace_style must be defined, which can be style ewald or pppm. The Ewald method was used in Streitz and diff --git a/doc/html/pair_coul_diel.html b/doc/html/pair_coul_diel.html index 88e078dfd5..1f7d3e04af 100644 --- a/doc/html/pair_coul_diel.html +++ b/doc/html/pair_coul_diel.html @@ -131,17 +131,17 @@ pair_style coul/diel/omp command Syntax - -pair_style coul/diel cutoff - +pair_style coul/diel cutoff + + cutoff = global cutoff (distance units) Examples - -pair_style coul/diel 3.5 -pair_coeff 1 4 78. 1.375 0.112 - +pair_style coul/diel 3.5 +pair_coeff 1 4 78. 1.375 0.112 + + Description diff --git a/doc/html/pair_cs.html b/doc/html/pair_cs.html index 12d0c515ef..75b462f741 100644 --- a/doc/html/pair_cs.html +++ b/doc/html/pair_cs.html @@ -131,9 +131,9 @@ pair_style buck/coul/long/cs command Syntax - -pair_style style args - +pair_style style args + + style = born/coul/long/cs or buck/coul/long/cs args = list of arguments for a particular style @@ -149,16 +149,16 @@ pair_style style args Examples - -pair_style born/coul/long/cs 10.0 8.0 -pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 - - -pair_style buck/coul/long/cs 10.0 -pair_style buck/coul/long/cs 10.0 8.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff 1 1 100.0 1.5 200.0 9.0 - +pair_style born/coul/long/cs 10.0 8.0 +pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 + + +pair_style buck/coul/long/cs 10.0 +pair_style buck/coul/long/cs 10.0 8.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff 1 1 100.0 1.5 200.0 9.0 + + Description diff --git a/doc/html/pair_dipole.html b/doc/html/pair_dipole.html index 25e82fc6e3..a8b5437180 100644 --- a/doc/html/pair_dipole.html +++ b/doc/html/pair_dipole.html @@ -149,12 +149,12 @@ pair_style lj/long/dipole/long command Syntax - -pair_style lj/cut/dipole/cut cutoff (cutoff2) -pair_style lj/sf/dipole/sf cutoff (cutoff2) -pair_style lj/cut/dipole/long cutoff (cutoff2) -pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2) - +pair_style lj/cut/dipole/cut cutoff (cutoff2) +pair_style lj/sf/dipole/sf cutoff (cutoff2) +pair_style lj/cut/dipole/long cutoff (cutoff2) +pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2) + + cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units) @@ -175,26 +175,26 @@ pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2) Examples - -pair_style lj/cut/dipole/cut 10.0 -pair_coeff * * 1.0 1.0 -pair_coeff 2 3 1.0 1.0 2.5 4.0 - - -pair_style lj/sf/dipole/sf 9.0 -pair_coeff * * 1.0 1.0 -pair_coeff 2 3 1.0 1.0 2.5 4.0 - - -pair_style lj/cut/dipole/long 10.0 -pair_coeff * * 1.0 1.0 -pair_coeff 2 3 1.0 1.0 2.5 4.0 - - -pair_style lj/long/dipole/long long long 3.5 10.0 -pair_coeff * * 1.0 1.0 -pair_coeff 2 3 1.0 1.0 2.5 4.0 - +pair_style lj/cut/dipole/cut 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 2 3 1.0 1.0 2.5 4.0 + + +pair_style lj/sf/dipole/sf 9.0 +pair_coeff * * 1.0 1.0 +pair_coeff 2 3 1.0 1.0 2.5 4.0 + + +pair_style lj/cut/dipole/long 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 2 3 1.0 1.0 2.5 4.0 + + +pair_style lj/long/dipole/long long long 3.5 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 2 3 1.0 1.0 2.5 4.0 + + Description diff --git a/doc/html/pair_dpd.html b/doc/html/pair_dpd.html index 1275469c41..f605baaa87 100644 --- a/doc/html/pair_dpd.html +++ b/doc/html/pair_dpd.html @@ -143,10 +143,10 @@ pair_style dpd/tstat/omp command Syntax - -pair_style dpd T cutoff seed -pair_style dpd/tstat Tstart Tstop cutoff seed - +pair_style dpd T cutoff seed +pair_style dpd/tstat Tstart Tstop cutoff seed + + T = temperature (temperature units) Tstart,Tstop = desired temperature at start/end of run (temperature units) @@ -156,16 +156,16 @@ pair_style dpd/tstat Tstart Tstop cutoff seed Examples - -pair_style dpd 1.0 2.5 34387 -pair_coeff * * 3.0 1.0 -pair_coeff 1 1 3.0 1.0 1.0 - - -pair_style dpd/tstat 1.0 1.0 2.5 34387 -pair_coeff * * 1.0 -pair_coeff 1 1 1.0 1.0 - +pair_style dpd 1.0 2.5 34387 +pair_coeff * * 3.0 1.0 +pair_coeff 1 1 3.0 1.0 1.0 + + +pair_style dpd/tstat 1.0 1.0 2.5 34387 +pair_coeff * * 1.0 +pair_coeff 1 1 1.0 1.0 + + Description diff --git a/doc/html/pair_dpd_fdt.html b/doc/html/pair_dpd_fdt.html index e6132b19d2..cd8033694c 100644 --- a/doc/html/pair_dpd_fdt.html +++ b/doc/html/pair_dpd_fdt.html @@ -131,9 +131,9 @@ pair_style dpd/fdt/energy command Syntax - -pair_style style args - +pair_style style args + + style = dpd/fdt or dpd/fdt/energy args = list of arguments for a particular style @@ -150,14 +150,14 @@ pair_style style args Examples - -pair_style dpd/fdt 300.0 2.5 34387 -pair_coeff * * 3.0 1.0 2.5 - - -pair_style dpd/fdt/energy 2.5 34387 -pair_coeff * * 3.0 1.0 0.1 2.5 - +pair_style dpd/fdt 300.0 2.5 34387 +pair_coeff * * 3.0 1.0 2.5 + + +pair_style dpd/fdt/energy 2.5 34387 +pair_coeff * * 3.0 1.0 0.1 2.5 + + Description diff --git a/doc/html/pair_eam.html b/doc/html/pair_eam.html index 62a0305a0c..81abf57a5a 100644 --- a/doc/html/pair_eam.html +++ b/doc/html/pair_eam.html @@ -176,32 +176,32 @@ pair_style eam/fs/opt command Syntax - -pair_style style - +pair_style style + + style = eam or eam/alloy or eam/cd or eam/fs Examples - -pair_style eam -pair_coeff * * cuu3 -pair_coeff 1*3 1*3 niu3.eam - - -pair_style eam/alloy -pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni - - -pair_style eam/cd -pair_coeff * * ../potentials/FeCr.cdeam Fe Cr - - -pair_style eam/fs -pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni - +pair_style eam +pair_coeff * * cuu3 +pair_coeff 1*3 1*3 niu3.eam + + +pair_style eam/alloy +pair_coeff * * ../potentials/NiAlH_jea.eam.alloy Ni Al Ni Ni + + +pair_style eam/cd +pair_coeff * * ../potentials/FeCr.cdeam Fe Cr + + +pair_style eam/fs +pair_coeff * * NiAlH_jea.eam.fs Ni Al Ni Ni + + Description @@ -270,9 +270,9 @@ single argument: filename Thus the following command - -pair_coeff *2 1*2 cuu3.eam - +pair_coeff *2 1*2 cuu3.eam + + will read the cuu3 potential file and use the tabulated Cu values for F, phi, rho that it contains for type pairs 1,1 and 2,2 (type pairs 1,2 and 2,1 are ignored). See the pair_coeff doc @@ -315,9 +315,9 @@ density). The units for the effective charge Z are “atomic charge” sqrt(Hartree * Bohr-radii). For two interacting atoms i,j this is used by LAMMPS to compute the pair potential term in the EAM energy expression as r*phi, in units of eV-Angstroms, via the formula - -r*phi = 27.2 * 0.529 * Zi * Zj - +r*phi = 27.2 * 0.529 * Zi * Zj + + where 1 Hartree = 27.2 eV and 1 Bohr = 0.529 Angstroms. Style eam/alloy computes pairwise interactions using the same @@ -350,9 +350,9 @@ page for alternate ways to specify the path for the potential file. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Ni, and the 4th to be Al, you would use the following pair_coeff command: - -pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al - +pair_coeff * * NiAlH_jea.eam.alloy Ni Ni Ni Al + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Ni arguments map LAMMPS atom types 1,2,3 to the Ni element in the setfl file. The final Al argument maps LAMMPS atom @@ -446,9 +446,9 @@ require that; the user can tabulate any functional form desired in the FS potential files. For style eam/fs, the form of the pair_coeff command is exactly the same as for style eam/alloy, e.g. - -pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al - +pair_coeff * * NiAlH_jea.eam.fs Ni Ni Ni Al + + where there are N additional arguments after the filename, where N is the number of LAMMPS atom types. See the pair_coeff doc page for alternate ways to specify the path for the potential diff --git a/doc/html/pair_edip.html b/doc/html/pair_edip.html index 54a690dde1..8c9d9ccdee 100644 --- a/doc/html/pair_edip.html +++ b/doc/html/pair_edip.html @@ -128,12 +128,12 @@ pair_style edip command Syntax - -pair_style edip - - -pair_style edip/omp - +pair_style edip + + +pair_style edip/omp + + Examples diff --git a/doc/html/pair_eff.html b/doc/html/pair_eff.html index 939cdbbf5c..6bcd28cef2 100644 --- a/doc/html/pair_eff.html +++ b/doc/html/pair_eff.html @@ -128,9 +128,9 @@ pair_style eff/cut command Syntax - -pair_style eff/cut cutoff keyword args ... - +pair_style eff/cut cutoff keyword args ... + + cutoff = global cutoff for Coulombic interactions zero or more keyword/value pairs may be appended @@ -146,16 +146,16 @@ keyword = limit/eradius or pressure/evirials or ecp Examples - -pair_style eff/cut 39.7 -pair_style eff/cut 40.0 limit/eradius -pair_style eff/cut 40.0 limit/eradius pressure/evirials -pair_style eff/cut 40.0 ecp 1 Si 3 C -pair_coeff * * -pair_coeff 2 2 20.0 -pair_coeff 1 s 0.320852 2.283269 0.814857 -pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621 - +pair_style eff/cut 39.7 +pair_style eff/cut 40.0 limit/eradius +pair_style eff/cut 40.0 limit/eradius pressure/evirials +pair_style eff/cut 40.0 ecp 1 Si 3 C +pair_coeff * * +pair_coeff 2 2 20.0 +pair_coeff 1 s 0.320852 2.283269 0.814857 +pair_coeff 3 p 22.721015 0.728733 1.103199 17.695345 6.693621 + + Description diff --git a/doc/html/pair_eim.html b/doc/html/pair_eim.html index 831c9f00dc..62c5a4a918 100644 --- a/doc/html/pair_eim.html +++ b/doc/html/pair_eim.html @@ -131,21 +131,21 @@ pair_style eim/omp command Syntax - -pair_style style - +pair_style style + + style = eim Examples - -pair_style eim -pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl -pair_coeff * * Na Cl ffield.eim Na Na Na Cl -pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na - +pair_style eim +pair_coeff * * Na Cl ../potentials/ffield.eim Na Cl +pair_coeff * * Na Cl ffield.eim Na Na Na Cl +pair_coeff * * Na Cl ../potentials/ffield.eim Cl NULL Na + + Description @@ -207,9 +207,9 @@ to specify the path for the potential file. system with Na and Cl atoms. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Na, and the 4th to be Cl, you would use the following pair_coeff command: - -pair_coeff * * Na Cl ffield.eim Na Na Na Cl - +pair_coeff * * Na Cl ffield.eim Na Na Na Cl + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The filename is the EIM potential file. The Na and Cl arguments (before the file name) are the two elements for which info will be diff --git a/doc/html/pair_exp6_rx.html b/doc/html/pair_exp6_rx.html index 79f0a9b4ae..6bd4ae6865 100644 --- a/doc/html/pair_exp6_rx.html +++ b/doc/html/pair_exp6_rx.html @@ -128,21 +128,21 @@ pair_style exp6/rx command Syntax - -pair_style exp6/rx cutoff - +pair_style exp6/rx cutoff + + cutoff = global cutoff for DPD interactions (distance units) Examples - -pair_style exp6/rx 10.0 -pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0 -pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0 -pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 - +pair_style exp6/rx 10.0 +pair_coeff * * exp6.params h2o h2o 1.0 1.0 10.0 +pair_coeff * * exp6.params h2o 1fluid 1.0 1.0 10.0 +pair_coeff * * exp6.params 1fluid 1fluid 1.0 1.0 10.0 + + Description diff --git a/doc/html/pair_gauss.html b/doc/html/pair_gauss.html index d90d449b83..2f167476f8 100644 --- a/doc/html/pair_gauss.html +++ b/doc/html/pair_gauss.html @@ -140,25 +140,25 @@ pair_style gauss/cut/omp command Syntax - -pair_style gauss cutoff -pair_style gauss/cut cutoff - +pair_style gauss cutoff +pair_style gauss/cut cutoff + + cutoff = global cutoff for Gauss interactions (distance units) Examples - -pair_style gauss 12.0 -pair_coeff * * 1.0 0.9 -pair_coeff 1 4 1.0 0.9 10.0 - - -pair_style gauss/cut 3.5 -pair_coeff 1 4 0.2805 1.45 0.112 - +pair_style gauss 12.0 +pair_coeff * * 1.0 0.9 +pair_coeff 1 4 1.0 0.9 10.0 + + +pair_style gauss/cut 3.5 +pair_coeff 1 4 0.2805 1.45 0.112 + + Description @@ -239,11 +239,11 @@ sites have an atom within the distance at which the force is a maximum = sqrt(0.5/b). This quantity can be accessed via the compute pair command as a vector of values of length 1. To print this quantity to the log file (with a descriptive column heading) the following commands could be included in an input script: - -compute gauss all pair gauss -variable occ equal c_gauss[1] -thermo_style custom step temp epair v_occ - +compute gauss all pair gauss +variable occ equal c_gauss[1] +thermo_style custom step temp epair v_occ + + diff --git a/doc/html/pair_gayberne.html b/doc/html/pair_gayberne.html index 68e46bd2d8..0b02a49a51 100644 --- a/doc/html/pair_gayberne.html +++ b/doc/html/pair_gayberne.html @@ -137,9 +137,9 @@ pair_style gayberne/omp command Syntax - -pair_style gayberne gamma upsilon mu cutoff - +pair_style gayberne gamma upsilon mu cutoff + + gamma = shift for potential minimum (typically 1) upsilon = exponent for eta orientation-dependent energy function @@ -149,10 +149,10 @@ pair_style gayberne gamma upsilon mu cutoff Examples - -pair_style gayberne 1.0 1.0 1.0 10.0 -pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 - +pair_style gayberne 1.0 1.0 1.0 10.0 +pair_coeff * * 1.0 1.7 1.7 3.4 3.4 1.0 1.0 1.0 + + Description diff --git a/doc/html/pair_gromacs.html b/doc/html/pair_gromacs.html index a58a10912a..7cc3aee2ce 100644 --- a/doc/html/pair_gromacs.html +++ b/doc/html/pair_gromacs.html @@ -140,9 +140,9 @@ pair_style lj/gromacs/coul/gromacs/omp command Syntax - -pair_style style args - +pair_style style args + + style = lj/gromacs or lj/gromacs/coul/gromacs args = list of arguments for a particular style @@ -157,16 +157,16 @@ pair_style style args Examples - -pair_style lj/gromacs 9.0 12.0 -pair_coeff * * 100.0 2.0 -pair_coeff 2 2 100.0 2.0 8.0 10.0 - - -pair_style lj/gromacs/coul/gromacs 9.0 12.0 -pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0 -pair_coeff * * 100.0 2.0 - +pair_style lj/gromacs 9.0 12.0 +pair_coeff * * 100.0 2.0 +pair_coeff 2 2 100.0 2.0 8.0 10.0 + + +pair_style lj/gromacs/coul/gromacs 9.0 12.0 +pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0 +pair_coeff * * 100.0 2.0 + + Description diff --git a/doc/html/pair_hbond_dreiding.html b/doc/html/pair_hbond_dreiding.html index e639ba34e8..659f637dec 100644 --- a/doc/html/pair_hbond_dreiding.html +++ b/doc/html/pair_hbond_dreiding.html @@ -137,9 +137,9 @@ pair_style hbond/dreiding/morse/omp command Syntax - -pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof - +pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof + + style = hbond/dreiding/lj or hbond/dreiding/morse n = cosine angle periodicity @@ -151,14 +151,14 @@ pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof Examples - -pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90 -pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0 - - -pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90 -pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 - +pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90 +pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0 + + +pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90 +pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90 + + Description @@ -265,7 +265,7 @@ follows: A single hydrogen atom type K can be specified, or a wild-card asterisk can be used in place of or in conjunction with the K arguments to select multiple types as hydrogens. This takes the form -“*” or “*n” or “n*” or “m*n”. See the pair_coeff command +“*” or “n” or “n” or “m*n”. See the pair_coeff command doc page for details. If the donor flag is i, then the atom of type I in the pair_coeff command is treated as the donor, and J is the acceptor. If the donor @@ -321,12 +321,12 @@ quantities can be accessed via the -compute hb all pair hbond/dreiding/lj -variable n_hbond equal c_hb[1] #number hbonds -variable E_hbond equal c_hb[2] #hbond energy -thermo_style custom step temp epair v_E_hbond - +compute hb all pair hbond/dreiding/lj +variable n_hbond equal c_hb[1] #number hbonds +variable E_hbond equal c_hb[2] #hbond energy +thermo_style custom step temp epair v_E_hbond + + diff --git a/doc/html/pair_list.html b/doc/html/pair_list.html index 2897df868b..f7d59aba21 100644 --- a/doc/html/pair_list.html +++ b/doc/html/pair_list.html @@ -128,9 +128,9 @@ pair_style list command Syntax - -pair_style list listfile cutoff keyword - +pair_style list listfile cutoff keyword + + listfile = name of file with list of pairwise interactions cutoff = global cutoff (distance units) @@ -139,15 +139,15 @@ pair_style list listfile cutoff keyword Examples - -pair_style list restraints.txt 200.0 -pair_coeff * * - - -pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0 -pair_coeff * * lj/cut 1.0 1.0 -pair_coeff 3* 3* list - +pair_style list restraints.txt 200.0 +pair_coeff * * + + +pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0 +pair_coeff * * lj/cut 1.0 1.0 +pair_coeff 3* 3* list + + Description diff --git a/doc/html/pair_lj.html b/doc/html/pair_lj.html index 73f9948c27..fd46ab5d3b 100644 --- a/doc/html/pair_lj.html +++ b/doc/html/pair_lj.html @@ -218,9 +218,9 @@ pair_style lj/cut/tip4p/long/opt command Syntax - -pair_style style args - +pair_style style args + + style = lj/cut or lj/cut/coul/cut or lj/cut/coul/debye or lj/cut/coul/dsf or lj/cut/coul/long or lj/cut/coul/long/cs or lj/cut/coul/msm or lj/cut/tip4p/long args = list of arguments for a particular style @@ -261,56 +261,56 @@ pair_style style args Examples - -pair_style lj/cut 2.5 -pair_coeff * * 1 1 -pair_coeff 1 1 1 1.1 2.8 - - -pair_style lj/cut/coul/cut 10.0 -pair_style lj/cut/coul/cut 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 -pair_coeff 1 1 100.0 3.5 9.0 9.0 - - -pair_style lj/cut/coul/debye 1.5 3.0 -pair_style lj/cut/coul/debye 1.5 2.5 5.0 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.5 2.5 -pair_coeff 1 1 1.0 1.5 2.5 5.0 - - -pair_style lj/cut/coul/dsf 0.05 2.5 10.0 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.0 2.5 - - -pair_style lj/cut/coul/long 10.0 -pair_style lj/cut/coul/long/cs 10.0 -pair_style lj/cut/coul/long 10.0 8.0 -pair_style lj/cut/coul/long/cs 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - - -pair_style lj/cut/coul/msm 10.0 -pair_style lj/cut/coul/msm 10.0 8.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - - -pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 -pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - - -pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 -pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - +pair_style lj/cut 2.5 +pair_coeff * * 1 1 +pair_coeff 1 1 1 1.1 2.8 + + +pair_style lj/cut/coul/cut 10.0 +pair_style lj/cut/coul/cut 10.0 8.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 +pair_coeff 1 1 100.0 3.5 9.0 9.0 + + +pair_style lj/cut/coul/debye 1.5 3.0 +pair_style lj/cut/coul/debye 1.5 2.5 5.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.0 1.5 2.5 +pair_coeff 1 1 1.0 1.5 2.5 5.0 + + +pair_style lj/cut/coul/dsf 0.05 2.5 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.0 1.0 2.5 + + +pair_style lj/cut/coul/long 10.0 +pair_style lj/cut/coul/long/cs 10.0 +pair_style lj/cut/coul/long 10.0 8.0 +pair_style lj/cut/coul/long/cs 10.0 8.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + + +pair_style lj/cut/coul/msm 10.0 +pair_style lj/cut/coul/msm 10.0 8.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + + +pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 +pair_style lj/cut/tip4p/cut 1 2 7 8 0.15 12.0 10.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + + +pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 +pair_style lj/cut/tip4p/long 1 2 7 8 0.15 12.0 10.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + + Description diff --git a/doc/html/pair_lj96.html b/doc/html/pair_lj96.html index 3f7e8fdd9b..25b68df4b4 100644 --- a/doc/html/pair_lj96.html +++ b/doc/html/pair_lj96.html @@ -134,20 +134,20 @@ pair_style lj96/cut/omp command Syntax - -pair_style lj96/cut cutoff - +pair_style lj96/cut cutoff + + cutoff = global cutoff for lj96/cut interactions (distance units) Examples - -pair_style lj96/cut 2.5 -pair_coeff * * 1.0 1.0 4.0 -pair_coeff 1 1 1.0 1.0 - +pair_style lj96/cut 2.5 +pair_coeff * * 1.0 1.0 4.0 +pair_coeff 1 1 1.0 1.0 + + Description diff --git a/doc/html/pair_lj_cubic.html b/doc/html/pair_lj_cubic.html index 6dad5de332..6032650397 100644 --- a/doc/html/pair_lj_cubic.html +++ b/doc/html/pair_lj_cubic.html @@ -134,16 +134,16 @@ pair_style lj/cubic/omp command Syntax - -pair_style lj/cubic - +pair_style lj/cubic + + Examples - -pair_style lj/cubic -pair_coeff * * 1.0 0.8908987 - +pair_style lj/cubic +pair_coeff * * 1.0 0.8908987 + + Description diff --git a/doc/html/pair_lj_expand.html b/doc/html/pair_lj_expand.html index 69fc39c046..fef3f21c46 100644 --- a/doc/html/pair_lj_expand.html +++ b/doc/html/pair_lj_expand.html @@ -134,20 +134,20 @@ pair_style lj/expand/omp command Syntax - -pair_style lj/expand cutoff - +pair_style lj/expand cutoff + + cutoff = global cutoff for lj/expand interactions (distance units) Examples - -pair_style lj/expand 2.5 -pair_coeff * * 1.0 1.0 0.5 -pair_coeff 1 1 1.0 1.0 -0.2 2.0 - +pair_style lj/expand 2.5 +pair_coeff * * 1.0 1.0 0.5 +pair_coeff 1 1 1.0 1.0 -0.2 2.0 + + Description diff --git a/doc/html/pair_lj_long.html b/doc/html/pair_lj_long.html index 2256d2d48e..fd2fa29241 100644 --- a/doc/html/pair_lj_long.html +++ b/doc/html/pair_lj_long.html @@ -137,9 +137,9 @@ pair_style lj/long/tip4p/long command Syntax - -pair_style style args - +pair_style style args + + style = lj/long/coul/long or lj/long/tip4p/long args = list of arguments for a particular style @@ -171,19 +171,19 @@ pair_style style args Examples - -pair_style lj/long/coul/long cut off 2.5 -pair_style lj/long/coul/long cut long 2.5 4.0 -pair_style lj/long/coul/long long long 2.5 4.0 -pair_coeff * * 1 1 -pair_coeff 1 1 1 3 4 - - -pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 -pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0 -pair_coeff * * 100.0 3.0 -pair_coeff 1 1 100.0 3.5 9.0 - +pair_style lj/long/coul/long cut off 2.5 +pair_style lj/long/coul/long cut long 2.5 4.0 +pair_style lj/long/coul/long long long 2.5 4.0 +pair_coeff * * 1 1 +pair_coeff 1 1 1 3 4 + + +pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 +pair_style lj/long/tip4p/long long long 1 2 7 8 0.15 12.0 10.0 +pair_coeff * * 100.0 3.0 +pair_coeff 1 1 100.0 3.5 9.0 + + Description diff --git a/doc/html/pair_lj_sf.html b/doc/html/pair_lj_sf.html index b09ff7e036..8505d91cf5 100644 --- a/doc/html/pair_lj_sf.html +++ b/doc/html/pair_lj_sf.html @@ -131,20 +131,20 @@ pair_style lj/sf/omp command Syntax - -pair_style lj/sf cutoff - +pair_style lj/sf cutoff + + cutoff = global cutoff for Lennard-Jones interactions (distance units) Examples - -pair_style lj/sf 2.5 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.0 3.0 - +pair_style lj/sf 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 1.0 1.0 3.0 + + Description diff --git a/doc/html/pair_lj_smooth.html b/doc/html/pair_lj_smooth.html index 0973d95ff9..22565da2d7 100644 --- a/doc/html/pair_lj_smooth.html +++ b/doc/html/pair_lj_smooth.html @@ -131,9 +131,9 @@ pair_style lj/smooth/omp command Syntax - -pair_style lj/smooth Rin Rc - +pair_style lj/smooth Rin Rc + + Rin = inner cutoff beyond which force smoothing will be applied (distance units) Rc = outer cutoff for lj/smooth interactions (distance units) @@ -141,11 +141,11 @@ pair_style lj/smooth Rin Rc Examples - -pair_style lj/smooth 8.0 10.0 -pair_coeff * * 10.0 1.5 -pair_coeff 1 1 20.0 1.3 7.0 9.0 - +pair_style lj/smooth 8.0 10.0 +pair_coeff * * 10.0 1.5 +pair_coeff 1 1 20.0 1.3 7.0 9.0 + + Description diff --git a/doc/html/pair_lj_smooth_linear.html b/doc/html/pair_lj_smooth_linear.html index edd6d68386..f19e28551e 100644 --- a/doc/html/pair_lj_smooth_linear.html +++ b/doc/html/pair_lj_smooth_linear.html @@ -131,20 +131,20 @@ pair_style lj/smooth/linear/omp command Syntax - -pair_style lj/smooth/linear Rc - +pair_style lj/smooth/linear Rc + + Rc = cutoff for lj/smooth/linear interactions (distance units) Examples - -pair_style lj/smooth/linear 5.456108274435118 -pair_coeff * * 0.7242785984051078 2.598146797350056 -pair_coeff 1 1 20.0 1.3 9.0 - +pair_style lj/smooth/linear 5.456108274435118 +pair_coeff * * 0.7242785984051078 2.598146797350056 +pair_coeff 1 1 20.0 1.3 9.0 + + Description diff --git a/doc/html/pair_lj_soft.html b/doc/html/pair_lj_soft.html index f67e200935..e253536083 100644 --- a/doc/html/pair_lj_soft.html +++ b/doc/html/pair_lj_soft.html @@ -173,9 +173,9 @@ pair_style tip4p/long/soft/omp command Syntax - -pair_style style args - +pair_style style args + + style = lj/cut/soft or lj/cut/coul/cut/soft or lj/cut/coul/long/soft or lj/cut/tip4p/long/soft or lj/charmm/coul/long/soft or coul/cut/soft or coul/long/soft or tip4p/long/soft args = list of arguments for a particular style @@ -219,47 +219,47 @@ pair_style style args Examples - -pair_style lj/cut/soft 2.0 0.5 9.5 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 1.0 9.5 - - -pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 -pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 0.5 10.0 -pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5 - - -pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 -pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 0.0 10.0 -pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 - - -pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 -pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5 -pair_coeff * * 0.155 3.1536 1.0 -pair_coeff 1 1 0.155 3.1536 1.0 9.5 - - -pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 -pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0 -pair_coeff * * 0.28 3.1 1.0 -pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 - - -pair_style coul/long/soft 1.0 10.0 9.5 -pair_coeff * * 1.0 -pair_coeff 1 1 1.0 9.5 - - -pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 -pair_coeff * * 1.0 -pair_coeff 1 1 1.0 9.5 - +pair_style lj/cut/soft 2.0 0.5 9.5 +pair_coeff * * 0.28 3.1 1.0 +pair_coeff 1 1 0.28 3.1 1.0 9.5 + + +pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 +pair_style lj/cut/coul/cut/soft 2.0 0.5 10.0 9.5 9.5 +pair_coeff * * 0.28 3.1 1.0 +pair_coeff 1 1 0.28 3.1 0.5 10.0 +pair_coeff 1 1 0.28 3.1 0.5 10.0 9.5 + + +pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 +pair_style lj/cut/coul/long/soft 2.0 0.5 10.0 9.5 9.5 +pair_coeff * * 0.28 3.1 1.0 +pair_coeff 1 1 0.28 3.1 0.0 10.0 +pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 + + +pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 +pair_style lj/cut/tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 9.5 +pair_coeff * * 0.155 3.1536 1.0 +pair_coeff 1 1 0.155 3.1536 1.0 9.5 + + +pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 +pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0 +pair_coeff * * 0.28 3.1 1.0 +pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 + + +pair_style coul/long/soft 1.0 10.0 9.5 +pair_coeff * * 1.0 +pair_coeff 1 1 1.0 9.5 + + +pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8 +pair_coeff * * 1.0 +pair_coeff 1 1 1.0 9.5 + + Description diff --git a/doc/html/pair_lubricate.html b/doc/html/pair_lubricate.html index b415ee6c3a..2cae3906c3 100644 --- a/doc/html/pair_lubricate.html +++ b/doc/html/pair_lubricate.html @@ -137,9 +137,9 @@ pair_style lubricate/poly/omp command Syntax - -pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF - +pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF + + style = lubricate or lubricate/poly mu = dynamic viscosity (dynamic viscosity units) @@ -151,17 +151,17 @@ pair_style style mu flaglog flagfld cutinner cutoff flagHI flagVF flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms Examples: (all assume radius = 1) - -pair_style lubricate 1.5 1 1 2.01 2.5 -pair_coeff 1 1 2.05 2.8 -pair_coeff * * - - -pair_style lubricate 1.5 1 1 2.01 2.5 -pair_coeff * * -variable mu equal ramp(1,2) -fix 1 all adapt 1 pair lubricate mu * * v_mu - +pair_style lubricate 1.5 1 1 2.01 2.5 +pair_coeff 1 1 2.05 2.8 +pair_coeff * * + + +pair_style lubricate 1.5 1 1 2.01 2.5 +pair_coeff * * +variable mu equal ramp(1,2) +fix 1 all adapt 1 pair lubricate mu * * v_mu + + Description diff --git a/doc/html/pair_lubricateU.html b/doc/html/pair_lubricateU.html index deca70058e..4d518c72e8 100644 --- a/doc/html/pair_lubricateU.html +++ b/doc/html/pair_lubricateU.html @@ -131,9 +131,9 @@ pair_style lubricateU/poly command Syntax - -pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF - +pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF + + style = lubricateU or lubricateU/poly mu = dynamic viscosity (dynamic viscosity units) @@ -145,11 +145,11 @@ pair_style style mu flaglog cutinner cutoff gdot flagHI flagVF flagVF (optional) = 0/1 to exclude/include volume fraction corrections in the long-range isotropic terms Examples: (all assume radius = 1) - -pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1 -pair_coeff 1 1 2.05 2.8 -pair_coeff * * - +pair_style lubricateU 1.5 1 2.01 2.5 0.01 1 1 +pair_coeff 1 1 2.05 2.8 +pair_coeff * * + + Description diff --git a/doc/html/pair_mdf.html b/doc/html/pair_mdf.html index 477829e523..9f78149009 100644 --- a/doc/html/pair_mdf.html +++ b/doc/html/pair_mdf.html @@ -134,9 +134,9 @@ pair_style lennard/mdf command Syntax - -pair_style style args - +pair_style style args + + style = lj/mdf or buck/mdf or lennard/mdf args = list of arguments for a particular style @@ -155,21 +155,21 @@ pair_style style args Examples - -pair_style lj/mdf 2.5 3.0 -pair_coeff * * 1 1 -pair_coeff 1 1 1 1.1 2.8 3.0 3.2 - - -pair_style buck 2.5 3.0 -pair_coeff * * 100.0 1.5 200.0 -pair_coeff * * 100.0 1.5 200.0 3.0 3.5 - - -pair_style lennard/mdf 2.5 3.0 -pair_coeff * * 1 1 -pair_coeff 1 1 1 1.1 2.8 3.0 3.2 - +pair_style lj/mdf 2.5 3.0 +pair_coeff * * 1 1 +pair_coeff 1 1 1 1.1 2.8 3.0 3.2 + + +pair_style buck 2.5 3.0 +pair_coeff * * 100.0 1.5 200.0 +pair_coeff * * 100.0 1.5 200.0 3.0 3.5 + + +pair_style lennard/mdf 2.5 3.0 +pair_coeff * * 1 1 +pair_coeff 1 1 1 1.1 2.8 3.0 3.2 + + Description @@ -198,7 +198,7 @@ below: epsilon (energy units) sigma (distance units) r_m (distance units) -r_cut (distance units) +r_cut (distance units) For the buck/mdf pair_style, the potential energy, E(r), is the @@ -209,7 +209,7 @@ standard Buckingham potential: rho (distance units) C (energy-distance^6 units) r_m (distance units) -r_cut$ (distance units) +r_cut$ (distance units) For the lennard/mdf pair_style, the potential energy, E(r), is the @@ -223,7 +223,7 @@ commands, or by mixing as described below: A (energy-distance^12 units) B (energy-distance^6 units) r_m (distance units) -r_cut (distance units) +r_cut (distance units) Mixing, shift, table, tail correction, restart, rRESPA info: diff --git a/doc/html/pair_meam.html b/doc/html/pair_meam.html index e9ec4ac13b..4c704bc583 100644 --- a/doc/html/pair_meam.html +++ b/doc/html/pair_meam.html @@ -128,17 +128,17 @@ pair_style meam command Syntax - -pair_style meam - +pair_style meam + + Examples - -pair_style meam -pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si -pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni - +pair_style meam +pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si +pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni + + Description @@ -194,9 +194,9 @@ settings for a variety of elements. The potentials/sic.meam file has specific parameter settings for a Si and C alloy system. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: - -pair_coeff * * library.meam Si C sic.meam Si Si Si C - +pair_coeff * * library.meam Si C sic.meam Si Si Si C + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The two filenames are for the library and parameter file respectively. The Si and C arguments (between the file names) are the two elements @@ -390,14 +390,14 @@ parameter erose_form, can be used to modify the Rose energy function used to compute the pair potential. This function gives the energy of the reference state as a function of interatomic spacing. The form of this function is: - -astar = alpha * (r/re - 1.d0) -if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar) -if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar) -if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar) -a3 = repuls, astar < 0 -a3 = attrac, astar >= 0 - +astar = alpha * (r/re - 1.d0) +if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar) +if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar) +if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar) +a3 = repuls, astar < 0 +a3 = attrac, astar >= 0 + + Most published MEAM parameter sets use the default values attrac=repulse=0. Setting repuls=attrac=delta corresponds to the form used in several recent published MEAM parameter sets, such as (Valone) diff --git a/doc/html/pair_meam_spline.html b/doc/html/pair_meam_spline.html index d0f57e43cb..04957d08ca 100644 --- a/doc/html/pair_meam_spline.html +++ b/doc/html/pair_meam_spline.html @@ -131,17 +131,17 @@ pair_style meam/spline/omp Syntax - -pair_style meam/spline - +pair_style meam/spline + + Examples - -pair_style meam/spline -pair_coeff * * Ti.meam.spline Ti -pair_coeff * * Ti.meam.spline Ti Ti Ti - +pair_style meam/spline +pair_coeff * * Ti.meam.spline Ti +pair_coeff * * Ti.meam.spline Ti Ti Ti + + Description @@ -180,9 +180,9 @@ to specify the path for the potential file. your LAMMPS simulation has 3 atoms types and they are all to be treated with this potentials, you would use the following pair_coeff command: - -pair_coeff * * Ti.meam.spline Ti Ti Ti - +pair_coeff * * Ti.meam.spline Ti Ti Ti + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The three Ti arguments map LAMMPS atom types 1,2,3 to the Ti element in the potential file. If a mapping value is specified as NULL, the diff --git a/doc/html/pair_meam_sw_spline.html b/doc/html/pair_meam_sw_spline.html index f3b221fef6..2608d4c901 100644 --- a/doc/html/pair_meam_sw_spline.html +++ b/doc/html/pair_meam_sw_spline.html @@ -131,17 +131,17 @@ pair_style meam/sw/spline/omp Syntax - -pair_style meam/sw/spline - +pair_style meam/sw/spline + + Examples - -pair_style meam/sw/spline -pair_coeff * * Ti.meam.sw.spline Ti -pair_coeff * * Ti.meam.sw.spline Ti Ti Ti - +pair_style meam/sw/spline +pair_coeff * * Ti.meam.sw.spline Ti +pair_coeff * * Ti.meam.sw.spline Ti Ti Ti + + Description diff --git a/doc/html/pair_mgpt.html b/doc/html/pair_mgpt.html index 9ac4b2224d..b014cdeb42 100644 --- a/doc/html/pair_mgpt.html +++ b/doc/html/pair_mgpt.html @@ -128,20 +128,20 @@ pair_style mgpt command Syntax - -pair_style mgpt - +pair_style mgpt + + Examples - -pair_style mgpt -pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega -cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin -cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin -pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double -pair_coeff * * parmin potin Omega volpress yes nbody 12 - +pair_style mgpt +pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega +cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin +cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin +pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double +pair_coeff * * parmin potin Omega volpress yes nbody 12 + + Description diff --git a/doc/html/pair_mie.html b/doc/html/pair_mie.html index 517b4bbec6..cdab3eaf53 100644 --- a/doc/html/pair_mie.html +++ b/doc/html/pair_mie.html @@ -131,21 +131,21 @@ pair_style mie/cut/gpu command Syntax - -pair_style mie/cut cutoff - +pair_style mie/cut cutoff + + cutoff = global cutoff for mie/cut interactions (distance units) Examples - -pair_style mie/cut 10.0 -pair_coeff 1 1 0.72 3.40 23.00 6.66 -pair_coeff 2 2 0.30 3.55 12.65 6.00 -pair_coeff 1 2 0.46 3.32 16.90 6.31 - +pair_style mie/cut 10.0 +pair_coeff 1 1 0.72 3.40 23.00 6.66 +pair_coeff 2 2 0.30 3.55 12.65 6.00 +pair_coeff 1 2 0.46 3.32 16.90 6.31 + + Description diff --git a/doc/html/pair_morse.html b/doc/html/pair_morse.html index bcf7271af0..bac9a4aa44 100644 --- a/doc/html/pair_morse.html +++ b/doc/html/pair_morse.html @@ -146,9 +146,9 @@ pair_style morse/soft command Syntax - -pair_style style args - +pair_style style args + + style = morse or morse/smooth/linear or morse/soft args = list of arguments for a particular style @@ -170,11 +170,11 @@ pair_style style args pair_style morse/smooth/linear 2.5 pair_coeff * * 100.0 2.0 1.5 pair_coeff 1 1 100.0 2.0 1.5 3.0 - -pair_style morse/soft 4 0.9 10.0 -pair_coeff * * 100.0 2.0 1.5 1.0 -pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 - +pair_style morse/soft 4 0.9 10.0 +pair_coeff * * 100.0 2.0 1.5 1.0 +pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 + + Description diff --git a/doc/html/pair_multi_lucy.html b/doc/html/pair_multi_lucy.html index 4a16b32697..6835ef752e 100644 --- a/doc/html/pair_multi_lucy.html +++ b/doc/html/pair_multi_lucy.html @@ -128,9 +128,9 @@ pair_style multi/lucy command Syntax - -pair_style multi/lucy style N keyword ... - +pair_style multi/lucy style N keyword ... + + style = lookup or linear = method of interpolation N = use N values in lookup, linear tables @@ -138,10 +138,10 @@ pair_style multi/lucy style N keyword ... Examples - -pair_style multi/lucy linear 1000 -pair_coeff * * multibody.table ENTRY1 7.0 - +pair_style multi/lucy linear 1000 +pair_coeff * * multibody.table ENTRY1 7.0 + + Description @@ -196,15 +196,15 @@ defined as follows (without the parenthesized comments): # Density-dependent function (one or more comment or blank lines) - -DD-FUNCTION (keyword is first text on line) -N 500 R 1.0 10.0 (N, R, RSQ parameters) - (blank) -1 1.0 25.5 102.34 (index, density, energy/r^4, force) -2 1.02 23.4 98.5 -... -500 10.0 0.001 0.003 - +DD-FUNCTION (keyword is first text on line) +N 500 R 1.0 10.0 (N, R, RSQ parameters) + (blank) +1 1.0 25.5 102.34 (index, density, energy/r^4, force) +2 1.02 23.4 98.5 +... +500 10.0 0.001 0.003 + + A section begins with a non-blank line whose 1st character is not a “#”; blank lines or lines starting with “#” can be used as comments between sections. The first line begins with a keyword which diff --git a/doc/html/pair_multi_lucy_rx.html b/doc/html/pair_multi_lucy_rx.html index ca4b859cdd..380cdc22fa 100644 --- a/doc/html/pair_multi_lucy_rx.html +++ b/doc/html/pair_multi_lucy_rx.html @@ -128,9 +128,9 @@ pair_style multi/lucy/rx command Syntax - -pair_style multi/lucy/rx style N keyword ... - +pair_style multi/lucy/rx style N keyword ... + + style = lookup or linear = method of interpolation N = use N values in lookup, linear tables @@ -138,11 +138,11 @@ pair_style multi/lucy/rx style N keyword ... Examples - -pair_style multi/lucy/rx linear 1000 -pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0 -pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 - +pair_style multi/lucy/rx linear 1000 +pair_coeff * * multibody.table ENTRY1 h2o h2o 7.0 +pair_coeff * * multibody.table ENTRY1 h2o 1fluid 7.0 + + Description @@ -215,15 +215,15 @@ defined as follows (without the parenthesized comments): # Density-dependent function (one or more comment or blank lines) - -DD-FUNCTION (keyword is first text on line) -N 500 R 1.0 10.0 (N, R, RSQ parameters) - (blank) -1 1.0 25.5 102.34 (index, density, energy/r^4, force) -2 1.02 23.4 98.5 -... -500 10.0 0.001 0.003 - +DD-FUNCTION (keyword is first text on line) +N 500 R 1.0 10.0 (N, R, RSQ parameters) + (blank) +1 1.0 25.5 102.34 (index, density, energy/r^4, force) +2 1.02 23.4 98.5 +... +500 10.0 0.001 0.003 + + A section begins with a non-blank line whose 1st character is not a “#”; blank lines or lines starting with “#” can be used as comments between sections. The first line begins with a keyword which diff --git a/doc/html/pair_nb3b_harmonic.html b/doc/html/pair_nb3b_harmonic.html index a24bb092e7..59fe5effb2 100644 --- a/doc/html/pair_nb3b_harmonic.html +++ b/doc/html/pair_nb3b_harmonic.html @@ -131,16 +131,16 @@ pair_style nb3b/harmonic/omp command Syntax - -pair_style nb3b/harmonic - +pair_style nb3b/harmonic + + Examples - -pair_style nb3b/harmonic -pair_coeff * * MgOH.nb3bharmonic Mg O H - +pair_style nb3b/harmonic +pair_coeff * * MgOH.nb3bharmonic Mg O H + + Description @@ -166,9 +166,9 @@ to specify the path for the potential file. for Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: - -pair_coeff * * SiC.nb3b.harmonic Si Si Si C - +pair_coeff * * SiC.nb3b.harmonic Si Si Si C + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the potential file. The final C argument maps LAMMPS atom diff --git a/doc/html/pair_nm.html b/doc/html/pair_nm.html index c7759721cf..10052c9d20 100644 --- a/doc/html/pair_nm.html +++ b/doc/html/pair_nm.html @@ -143,9 +143,9 @@ pair_style nm/cut/coul/long/omp command Syntax - -pair_style style args - +pair_style style args + + style = nm/cut or nm/cut/coul/cut or nm/cut/coul/long args = list of arguments for a particular style @@ -163,21 +163,21 @@ pair_style style args Examples - -pair_style nm/cut 12.0 -pair_coeff * * 0.01 5.4 8.0 7.0 -pair_coeff 1 1 0.01 4.4 7.0 6.0 - - -pair_style nm/cut/coul/cut 12.0 15.0 -pair_coeff * * 0.01 5.4 8.0 7.0 -pair_coeff 1 1 0.01 4.4 7.0 6.0 - - -pair_style nm/cut/coul/long 12.0 15.0 -pair_coeff * * 0.01 5.4 8.0 7.0 -pair_coeff 1 1 0.01 4.4 7.0 6.0 - +pair_style nm/cut 12.0 +pair_coeff * * 0.01 5.4 8.0 7.0 +pair_coeff 1 1 0.01 4.4 7.0 6.0 + + +pair_style nm/cut/coul/cut 12.0 15.0 +pair_coeff * * 0.01 5.4 8.0 7.0 +pair_coeff 1 1 0.01 4.4 7.0 6.0 + + +pair_style nm/cut/coul/long 12.0 15.0 +pair_coeff * * 0.01 5.4 8.0 7.0 +pair_coeff 1 1 0.01 4.4 7.0 6.0 + + Description diff --git a/doc/html/pair_polymorphic.html b/doc/html/pair_polymorphic.html index 017a5148d0..550805f4da 100644 --- a/doc/html/pair_polymorphic.html +++ b/doc/html/pair_polymorphic.html @@ -128,20 +128,20 @@ pair_style polymorphic command Syntax - -pair_style polymorphic - +pair_style polymorphic + + style = polymorphic Examples - -pair_style polymorphic -pair_coeff * * TlBr_msw.polymorphic Tl Br -pair_coeff * * AlCu_eam.polymorphic Al Cu -pair_coeff * * GaN_tersoff.polymorphic Ga N -pair_coeff * * GaN_sw.polymorphic GaN - +pair_style polymorphic +pair_coeff * * TlBr_msw.polymorphic Tl Br +pair_coeff * * AlCu_eam.polymorphic Al Cu +pair_coeff * * GaN_tersoff.polymorphic Ga N +pair_coeff * * GaN_sw.polymorphic GaN + + Description @@ -210,9 +210,9 @@ included in the potentials dir of the LAMMPS distro. They have a functions for Si-C tersoff potential. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: - -pair_coeff * * SiC_tersoff.polymorphic Si Si Si C - +pair_coeff * * SiC_tersoff.polymorphic Si Si Si C + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the polymorphic file. The final C argument maps LAMMPS @@ -235,19 +235,19 @@ eta_ij defined in the potential functions above is set to 1 - delta_ij, otherwise eta_ij is set to delta_ij. The next ntypes lines each lists two numbers and a character string representing atomic number, atomic mass, and name of the species of the ntypes elements: - -atomic_number atomic-mass element (1) -atomic_number atomic-mass element (2) -... -atomic_number atomic-mass element (ntypes) - +atomic_number atomic-mass element (1) +atomic_number atomic-mass element (2) +... +atomic_number atomic-mass element (ntypes) + + The next ntypes*(ntypes+1)/2 lines contain two numbers: - -cut xi (1) -cut xi (2) -... -cut xi (ntypes*(ntypes+1)/2) - +cut xi (1) +cut xi (2) +... +cut xi (ntypes*(ntypes+1)/2) + + Here cut means the cutoff distance of the pair functions, xi is the same as defined in the potential functions above. The ntypes*(ntypes+1)/2 lines are related to the pairs according to the diff --git a/doc/html/pair_resquared.html b/doc/html/pair_resquared.html index 70c4fd0ba0..edf33d6bdb 100644 --- a/doc/html/pair_resquared.html +++ b/doc/html/pair_resquared.html @@ -134,19 +134,19 @@ pair_style resquared/omp command Syntax - -pair_style resquared cutoff - +pair_style resquared cutoff + + cutoff = global cutoff for interactions (distance units) Examples - -pair_style resquared 10.0 -pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 - +pair_style resquared 10.0 +pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 + + Description diff --git a/doc/html/pair_sdk.html b/doc/html/pair_sdk.html index 21a9ded1a5..a8cfc33d42 100644 --- a/doc/html/pair_sdk.html +++ b/doc/html/pair_sdk.html @@ -146,9 +146,9 @@ pair_style lj/sdk/coul/long/omp command Syntax - -pair_style style args - +pair_style style args + + style = lj/sdk or lj/sdk/coul/long args = list of arguments for a particular style @@ -163,15 +163,15 @@ pair_style style args Examples - -pair_style lj/sdk 2.5 -pair_coeff 1 1 lj12_6 1 1.1 2.8 - - -pair_style lj/sdk/coul/long 10.0 -pair_style lj/sdk/coul/long 10.0 12.0 -pair_coeff 1 1 lj9_6 100.0 3.5 12.0 - +pair_style lj/sdk 2.5 +pair_coeff 1 1 lj12_6 1 1.1 2.8 + + +pair_style lj/sdk/coul/long 10.0 +pair_style lj/sdk/coul/long 10.0 12.0 +pair_coeff 1 1 lj9_6 100.0 3.5 12.0 + + Description diff --git a/doc/html/pair_smtbq.html b/doc/html/pair_smtbq.html index f9b3de8f22..568539fd0c 100644 --- a/doc/html/pair_smtbq.html +++ b/doc/html/pair_smtbq.html @@ -128,16 +128,16 @@ pair_style smtbq command Syntax - -pair_style smtbq - +pair_style smtbq + + Examples - -pair_style smtbq -pair_coeff * * ffield.smtbq.Al2O3 O Al - +pair_style smtbq +pair_coeff * * ffield.smtbq.Al2O3 O Al + + Description @@ -164,9 +164,9 @@ filename in the pair_coeff command. Note that atom type 1 must always correspond to oxygen atoms. As an example, to simulate a TiO2 system, atom type 1 has to be oxygen and atom type 2 Ti. The following pair_coeff command should then be used: - -pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti - +pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti + + The electrostatic part of the energy consists of two components self-energy of atom i in the form of a second order charge dependent polynomial and a long-range Coulombic electrostatic interaction. The @@ -271,7 +271,7 @@ quotation marks (‘’). Keyword for element1, element2 and interaction potential (‘second_moment’ or ‘buck’ or ‘buckPlusAttr’) between element 1 and 2. If the potential is ‘second_moment’, specify ‘oxide’ or ‘metal’ for metal-oxygen or metal-metal interactions respectively. -Potential parameter: <pre><br/> If type of potential is ‘second_moment’ : A (eV), p, ξ<sup>0</sup> (eV) and q <br/> r<sub>c1</sub> (Å), r<sub>c2</sub> (Å) and r<sub>0</sub> (Å) <br/> If type of potential is ‘buck’ : C (eV) and ρ (Å) <br/> If type of potential is ‘buckPlusAttr’ : C (eV) and ρ (Å) <br/> D (eV), B (Å<sup>-1</sup>), r<sub>1</sub><sup>OO</sup> (Å) and r<sub>2</sub><sup>OO</sup> (Å) </pre> +Potential parameter: <pre><br/> If type of potential is ‘second_moment’ : A (eV), p, ξ<sup>0</sup> (eV) and q <br/> r<sub>c1</sub> (Å), r<sub>c2</sub> (Å) and r<sub>0</sub> (Å) <br/> If type of potential is ‘buck’ : C (eV) and ρ (Å) <br/> If type of potential is ‘buckPlusAttr’ : C (eV) and ρ (Å) <br/> D (eV), B (Å<sup>-1</sup>), r<sub>1</sub><sup>OO</sup> (Å) and r<sub>2</sub><sup>OO</sup> (Å) </pre> Divided line diff --git a/doc/html/pair_snap.html b/doc/html/pair_snap.html index 0589cb40a5..bc82ce506e 100644 --- a/doc/html/pair_snap.html +++ b/doc/html/pair_snap.html @@ -128,16 +128,16 @@ pair_style snap command Syntax - -pair_style snap - +pair_style snap + + Examples - -pair_style snap -pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P - +pair_style snap +pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P + + Description @@ -180,9 +180,9 @@ command, where N is the number of LAMMPS atom types: As an example, if a LAMMPS indium phosphide simulation has 4 atoms types, with the first two being indium and the 3rd and 4th being phophorous, the pair_coeff command would look like this: - -pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P - +pair_coeff * * snap InP.snapcoeff In P InP.snapparam In In P P + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The two filenames are for the element and parameter files, respectively. The ‘In’ and ‘P’ arguments (between the file names) are the two elements @@ -210,8 +210,7 @@ using the hybrid/overlay pair style. As an example, the SNAP tantalum potential provided in the LAMMPS potentials directory combines the snap and zbl pair styles. It is invoked by the following commands: - -variable zblcutinner equal 4 +variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 73 pair_style hybrid/overlay & @@ -220,7 +219,8 @@ pair_coeff * * zbl 0.0 pair_coeff 1 1 zbl ${zblz} pair_coeff * * snap ../potentials/Ta06A.snapcoeff Ta & ../potentials/Ta06A.snapparam Ta - + + It is convenient to keep these commands in a separate file that can be inserted in any LAMMPS input script using the include command. diff --git a/doc/html/pair_soft.html b/doc/html/pair_soft.html index 3443927106..0929a1f6af 100644 --- a/doc/html/pair_soft.html +++ b/doc/html/pair_soft.html @@ -134,26 +134,26 @@ pair_style soft/omp command Syntax - -pair_style soft cutoff - +pair_style soft cutoff + + cutoff = global cutoff for soft interactions (distance units) Examples - -pair_style soft 1.0 -pair_coeff * * 10.0 -pair_coeff 1 1 10.0 3.0 - - -pair_style soft 1.0 -pair_coeff * * 0.0 -variable prefactor equal ramp(0,30) -fix 1 all adapt 1 pair soft a * * v_prefactor - +pair_style soft 1.0 +pair_coeff * * 10.0 +pair_coeff 1 1 10.0 3.0 + + +pair_style soft 1.0 +pair_coeff * * 0.0 +variable prefactor equal ramp(0,30) +fix 1 all adapt 1 pair soft a * * v_prefactor + + Description @@ -193,10 +193,10 @@ pair_coeff settings for A must still be specified, but will be overridden. For example these commands will vary the prefactor A for all pairwise interactions from 0.0 at the beginning to 30.0 at the end of a run: - -variable prefactor equal ramp(0,30) -fix 1 all adapt 1 pair soft a * * v_prefactor - +variable prefactor equal ramp(0,30) +fix 1 all adapt 1 pair soft a * * v_prefactor + + Note that a formula defined by an equal-style variable can use the current timestep, elapsed time in the current run, elapsed time since the beginning of a series of runs, as well as access other diff --git a/doc/html/pair_sph_idealgas.html b/doc/html/pair_sph_idealgas.html index 602e66a277..130c193d90 100644 --- a/doc/html/pair_sph_idealgas.html +++ b/doc/html/pair_sph_idealgas.html @@ -128,16 +128,16 @@ pair_style sph/idealgas command Syntax - -pair_style sph/idealgas - +pair_style sph/idealgas + + Examples - -pair_style sph/idealgas -pair_coeff * * 1.0 2.4 - +pair_style sph/idealgas +pair_coeff * * 1.0 2.4 + + Description diff --git a/doc/html/pair_sph_taitwater.html b/doc/html/pair_sph_taitwater.html index 0ce7b08918..0d56ce2bdd 100644 --- a/doc/html/pair_sph_taitwater.html +++ b/doc/html/pair_sph_taitwater.html @@ -128,16 +128,16 @@ pair_style sph/taitwater command Syntax - -pair_style sph/taitwater - +pair_style sph/taitwater + + Examples - -pair_style sph/taitwater -pair_coeff * * 1000.0 1430.0 1.0 2.4 - +pair_style sph/taitwater +pair_coeff * * 1000.0 1430.0 1.0 2.4 + + Description diff --git a/doc/html/pair_sph_taitwater_morris.html b/doc/html/pair_sph_taitwater_morris.html index fda93bd07c..8c6f8c913a 100644 --- a/doc/html/pair_sph_taitwater_morris.html +++ b/doc/html/pair_sph_taitwater_morris.html @@ -128,16 +128,16 @@ pair_style sph/taitwater/morris command Syntax - -pair_style sph/taitwater/morris - +pair_style sph/taitwater/morris + + Examples - -pair_style sph/taitwater/morris -pair_coeff * * 1000.0 1430.0 1.0 2.4 - +pair_style sph/taitwater/morris +pair_coeff * * 1000.0 1430.0 1.0 2.4 + + Description diff --git a/doc/html/pair_srp.html b/doc/html/pair_srp.html index a9e1607ab8..caddb4012a 100644 --- a/doc/html/pair_srp.html +++ b/doc/html/pair_srp.html @@ -143,24 +143,24 @@ Examples - -pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes -pair_coeff 1 1 dpd 60.0 4.5 1.0 -pair_coeff 1 2 none -pair_coeff 2 2 srp 100.0 0.8 - - -pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes -pair_coeff 1 1 dpd 60.0 50 1.0 -pair_coeff 1 2 none -pair_coeff 2 2 srp 40.0 - - -pair_style hybrid srp 0.8 2 mid -pair_coeff 1 1 none -pair_coeff 1 2 none -pair_coeff 2 2 srp 100.0 0.8 - +pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 1 mid exclude yes +pair_coeff 1 1 dpd 60.0 4.5 1.0 +pair_coeff 1 2 none +pair_coeff 2 2 srp 100.0 0.8 + + +pair_style hybrid dpd 1.0 1.0 12345 srp 0.8 * min exclude yes +pair_coeff 1 1 dpd 60.0 50 1.0 +pair_coeff 1 2 none +pair_coeff 2 2 srp 40.0 + + +pair_style hybrid srp 0.8 2 mid +pair_coeff 1 1 none +pair_coeff 1 2 none +pair_coeff 2 2 srp 100.0 0.8 + + Description diff --git a/doc/html/pair_sw.html b/doc/html/pair_sw.html index 687c162b34..099d2de727 100644 --- a/doc/html/pair_sw.html +++ b/doc/html/pair_sw.html @@ -140,17 +140,17 @@ pair_style sw/omp command Syntax - -pair_style sw - +pair_style sw + + Examples - -pair_style sw -pair_coeff * * si.sw Si -pair_coeff * * GaN.sw Ga N Ga - +pair_style sw +pair_coeff * * si.sw Si +pair_coeff * * GaN.sw Ga N Ga + + Description @@ -175,9 +175,9 @@ to specify the path for the potential file. Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: - -pair_coeff * * SiC.sw Si Si Si C - +pair_coeff * * SiC.sw Si Si Si C + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the SW file. The final C argument maps LAMMPS atom type 4 diff --git a/doc/html/pair_tersoff.html b/doc/html/pair_tersoff.html index 8345a1c90b..6ea2a43607 100644 --- a/doc/html/pair_tersoff.html +++ b/doc/html/pair_tersoff.html @@ -146,22 +146,22 @@ pair_style tersoff/table/omp command Syntax - -pair_style style - +pair_style style + + style = tersoff or tersoff/table or tersoff/gpu or tersoff/omp or tersoff/table/omp Examples - -pair_style tersoff -pair_coeff * * Si.tersoff Si -pair_coeff * * SiC.tersoff Si C Si - - -pair_style tersoff/table -pair_coeff * * SiCGe.tersoff Si(D) - +pair_style tersoff +pair_coeff * * Si.tersoff Si +pair_coeff * * SiC.tersoff Si C Si + + +pair_style tersoff/table +pair_coeff * * SiCGe.tersoff Si(D) + + Description @@ -191,9 +191,9 @@ to specify the path for the potential file. and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: - -pair_coeff * * SiC.tersoff Si Si Si C - +pair_coeff * * SiC.tersoff Si Si Si C + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the Tersoff file. The final C argument maps LAMMPS atom diff --git a/doc/html/pair_tersoff_mod.html b/doc/html/pair_tersoff_mod.html index 34a2120f67..b88d02ee18 100644 --- a/doc/html/pair_tersoff_mod.html +++ b/doc/html/pair_tersoff_mod.html @@ -137,16 +137,16 @@ pair_style tersoff/mod/omp command Syntax - -pair_style tersoff/mod - +pair_style tersoff/mod + + Examples - -pair_style tersoff/mod -pair_coeff * * Si.tersoff.mod Si Si - +pair_style tersoff/mod +pair_coeff * * Si.tersoff.mod Si Si + + Description @@ -180,9 +180,9 @@ where N is the number of LAMMPS atom types: As an example, imagine the Si.tersoff_mod file has Tersoff values for Si. If your LAMMPS simulation has 3 Si atoms types, you would use the following pair_coeff command: - -pair_coeff * * Si.tersoff_mod Si Si Si - +pair_coeff * * Si.tersoff_mod Si Si Si + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the Tersoff/MOD file. If a mapping value is specified as NULL, the diff --git a/doc/html/pair_tersoff_zbl.html b/doc/html/pair_tersoff_zbl.html index 694938f86e..90e840acc3 100644 --- a/doc/html/pair_tersoff_zbl.html +++ b/doc/html/pair_tersoff_zbl.html @@ -137,16 +137,16 @@ pair_style tersoff/zbl/omp command Syntax - -pair_style tersoff/zbl - +pair_style tersoff/zbl + + Examples - -pair_style tersoff/zbl -pair_coeff * * SiC.tersoff.zbl Si C Si - +pair_style tersoff/zbl +pair_coeff * * SiC.tersoff.zbl Si C Si + + Description @@ -188,9 +188,9 @@ to specify the path for the potential file. for Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: - -pair_coeff * * SiC.tersoff Si Si Si C - +pair_coeff * * SiC.tersoff Si Si Si C + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the Tersoff/ZBL file. The final C argument maps LAMMPS diff --git a/doc/html/pair_vashishta.html b/doc/html/pair_vashishta.html index 6dd3e02f8f..0bfaceb06c 100644 --- a/doc/html/pair_vashishta.html +++ b/doc/html/pair_vashishta.html @@ -131,16 +131,16 @@ pair_style vashishta/omp command Syntax - -pair_style vashishta - +pair_style vashishta + + Examples - -pair_style vashishta -pair_coeff * * SiC.vashishta Si C - +pair_style vashishta +pair_coeff * * SiC.vashishta Si C + + Description @@ -178,9 +178,9 @@ to specify the path for the potential file. Si and C. If your LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, and the 4th to be C, you would use the following pair_coeff command: - -pair_coeff * * SiC.vashishta Si Si Si C - +pair_coeff * * SiC.vashishta Si Si Si C + + The 1st 2 arguments must be * * so as to span all LAMMPS atom types. The first three Si arguments map LAMMPS atom types 1,2,3 to the Si element in the file. The final C argument maps LAMMPS atom type 4 diff --git a/doc/html/pair_yukawa.html b/doc/html/pair_yukawa.html index 3f0d3b3e2c..826c7de7ff 100644 --- a/doc/html/pair_yukawa.html +++ b/doc/html/pair_yukawa.html @@ -134,9 +134,9 @@ pair_style yukawa/omp command Syntax - -pair_style yukawa kappa cutoff - +pair_style yukawa kappa cutoff + + kappa = screening length (inverse distance units) cutoff = global cutoff for Yukawa interactions (distance units) @@ -144,11 +144,11 @@ pair_style yukawa kappa cutoff Examples - -pair_style yukawa 2.0 2.5 -pair_coeff 1 1 100.0 2.3 -pair_coeff * * 100.0 - +pair_style yukawa 2.0 2.5 +pair_coeff 1 1 100.0 2.3 +pair_coeff * * 100.0 + + Description diff --git a/doc/html/pair_yukawa_colloid.html b/doc/html/pair_yukawa_colloid.html index 0c16f65c1d..560d253325 100644 --- a/doc/html/pair_yukawa_colloid.html +++ b/doc/html/pair_yukawa_colloid.html @@ -134,9 +134,9 @@ pair_style yukawa/colloid/omp command Syntax - -pair_style yukawa/colloid kappa cutoff - +pair_style yukawa/colloid kappa cutoff + + kappa = screening length (inverse distance units) cutoff = global cutoff for colloidal Yukawa interactions (distance units) @@ -144,11 +144,11 @@ pair_style yukawa/colloid kappa cutoff Examples - -pair_style yukawa/colloid 2.0 2.5 -pair_coeff 1 1 100.0 2.3 -pair_coeff * * 100.0 - +pair_style yukawa/colloid 2.0 2.5 +pair_coeff 1 1 100.0 2.3 +pair_coeff * * 100.0 + + Description @@ -182,9 +182,9 @@ charge and surface potential due to the presence of electrolyte. Note that the A for this potential style has different units than the A used in pair_style yukawa. For low surface potentials, i.e. less than about 25 mV, A can be written as: - -A = 2 * PI * R*eps*eps0 * kappa * psi^2 - +A = 2 * PI * R*eps*eps0 * kappa * psi^2 + + where R = colloid radius (distance units) diff --git a/doc/html/pair_zbl.html b/doc/html/pair_zbl.html index 54ad6b5344..71b3bea35c 100644 --- a/doc/html/pair_zbl.html +++ b/doc/html/pair_zbl.html @@ -134,9 +134,9 @@ pair_style zbl/omp command Syntax - -pair_style zbl inner outer - +pair_style zbl inner outer + + inner = distance where switching function begins outer = global cutoff for ZBL interaction @@ -144,11 +144,11 @@ pair_style zbl inner outer Examples - -pair_style zbl 3.0 4.0 -pair_coeff * * 73.0 73.0 -pair_coeff 1 1 14.0 14.0 - +pair_style zbl 3.0 4.0 +pair_coeff * * 73.0 73.0 +pair_coeff 1 1 14.0 14.0 + + Description diff --git a/doc/src/fix_restrain.txt b/doc/src/fix_restrain.txt index 9655b7cb72..596ca54b67 100644 --- a/doc/src/fix_restrain.txt +++ b/doc/src/fix_restrain.txt @@ -41,15 +41,26 @@ fix texas_holdem all restrain dihedral 1 2 3 4 0.0 2000.0 120.0 dihedral 1 2 3 5 Restrain the motion of the specified sets of atoms by making them part of a bond or angle or dihedral interaction whose strength can vary -over time during a simulation. This is functionally equivalent to +over time during a simulation. This is functionally similar to creating a bond or angle or dihedral for the same atoms in a data file, as specified by the "read_data"_read_data.html command, albeit -with a time-varying pre-factor coefficient. For the purpose of -forcefield parameter-fitting or mapping a molecular potential energy -surface, this fix reduces the hassle and risk associated with -modifying data files. In other words, use this fix to temporarily -force a molecule to adopt a particular conformation. To create a -permanent bond or angle or dihedral, you should modify the data file. +with a time-varying pre-factor coefficient, and except for exclusion +rules, as explained below. + +For the purpose of forcefield parameter-fitting or mapping a molecular +potential energy surface, this fix reduces the hassle and risk +associated with modifying data files. In other words, use this fix to +temporarily force a molecule to adopt a particular conformation. To +create a permanent bond or angle or dihedral, you should modify the +data file. + +NOTE: Adding a bond/angle/dihedral with this command does not apply +the exclusion rules and weighting factors specified by the +"special_bonds"_special_bonds.html command to atoms in the restraint +that are now bonded (1-2,1-3,1-4 neighbors) as a result. If they are +close enough to interact in a "pair_style"_pair_style.html sense +(non-bonded interaction), then the bond/angle/dihedral restraint +interaction will simply be superposed on top of that interaction. The group-ID specified by this fix is ignored. diff --git a/src/KOKKOS/fix_qeq_reax_kokkos.h b/src/KOKKOS/fix_qeq_reax_kokkos.h index 2c8b7860ef..eca0d761b7 100644 --- a/src/KOKKOS/fix_qeq_reax_kokkos.h +++ b/src/KOKKOS/fix_qeq_reax_kokkos.h @@ -132,7 +132,9 @@ class FixQEqReaxKokkos : public FixQEqReax { double calculate_H_k(const F_FLOAT &r, const F_FLOAT &shld) const; struct params_qeq{ + KOKKOS_INLINE_FUNCTION params_qeq(){chi=0;eta=0;gamma=0;}; + KOKKOS_INLINE_FUNCTION params_qeq(int i){chi=0;eta=0;gamma=0;}; F_FLOAT chi, eta, gamma; }; diff --git a/src/KOKKOS/pair_reax_c_kokkos.cpp b/src/KOKKOS/pair_reax_c_kokkos.cpp index ea898843e7..4fcb3652e3 100644 --- a/src/KOKKOS/pair_reax_c_kokkos.cpp +++ b/src/KOKKOS/pair_reax_c_kokkos.cpp @@ -370,43 +370,43 @@ void PairReaxCKokkos::init_md() k_LR.h_view(i,j).a = LR[i][j].a; k_LR.h_view(i,j).m = LR[i][j].m; k_LR.h_view(i,j).c = LR[i][j].c; + + tdual_LR_data_1d k_y = tdual_LR_data_1d("lookup:LR[i,j].y",n); + tdual_cubic_spline_coef_1d k_H = tdual_cubic_spline_coef_1d("lookup:LR[i,j].H",n); + tdual_cubic_spline_coef_1d k_vdW = tdual_cubic_spline_coef_1d("lookup:LR[i,j].vdW",n); + tdual_cubic_spline_coef_1d k_CEvd = tdual_cubic_spline_coef_1d("lookup:LR[i,j].CEvd",n); + tdual_cubic_spline_coef_1d k_ele = tdual_cubic_spline_coef_1d("lookup:LR[i,j].ele",n); + tdual_cubic_spline_coef_1d k_CEclmb = tdual_cubic_spline_coef_1d("lookup:LR[i,j].CEclmb",n); - k_LR.h_view(i,j).k_y = tdual_LR_data_1d("lookup:LR[i,j].y",n); - k_LR.h_view(i,j).k_H = tdual_cubic_spline_coef_1d("lookup:LR[i,j].H",n); - k_LR.h_view(i,j).k_vdW = tdual_cubic_spline_coef_1d("lookup:LR[i,j].vdW",n); - k_LR.h_view(i,j).k_CEvd = tdual_cubic_spline_coef_1d("lookup:LR[i,j].CEvd",n); - k_LR.h_view(i,j).k_ele = tdual_cubic_spline_coef_1d("lookup:LR[i,j].ele",n); - k_LR.h_view(i,j).k_CEclmb = tdual_cubic_spline_coef_1d("lookup:LR[i,j].CEclmb",n); - - k_LR.h_view(i,j).d_y = k_LR.h_view(i,j).k_y.d_view; - k_LR.h_view(i,j).d_H = k_LR.h_view(i,j).k_H.d_view; - k_LR.h_view(i,j).d_vdW = k_LR.h_view(i,j).k_vdW.d_view; - k_LR.h_view(i,j).d_CEvd = k_LR.h_view(i,j).k_CEvd.d_view; - k_LR.h_view(i,j).d_ele = k_LR.h_view(i,j).k_ele.d_view; - k_LR.h_view(i,j).d_CEclmb = k_LR.h_view(i,j).k_CEclmb.d_view; + k_LR.h_view(i,j).d_y = k_y.d_view; + k_LR.h_view(i,j).d_H = k_H.d_view; + k_LR.h_view(i,j).d_vdW = k_vdW.d_view; + k_LR.h_view(i,j).d_CEvd = k_CEvd.d_view; + k_LR.h_view(i,j).d_ele = k_ele.d_view; + k_LR.h_view(i,j).d_CEclmb = k_CEclmb.d_view; for (int k = 0; k < n; k++) { - k_LR.h_view(i,j).k_y.h_view(k) = LR[i][j].y[k]; - k_LR.h_view(i,j).k_H.h_view(k) = LR[i][j].H[k]; - k_LR.h_view(i,j).k_vdW.h_view(k) = LR[i][j].vdW[k]; - k_LR.h_view(i,j).k_CEvd.h_view(k) = LR[i][j].CEvd[k]; - k_LR.h_view(i,j).k_ele.h_view(k) = LR[i][j].ele[k]; - k_LR.h_view(i,j).k_CEclmb.h_view(k) = LR[i][j].CEclmb[k]; + k_y.h_view(k) = LR[i][j].y[k]; + k_H.h_view(k) = LR[i][j].H[k]; + k_vdW.h_view(k) = LR[i][j].vdW[k]; + k_CEvd.h_view(k) = LR[i][j].CEvd[k]; + k_ele.h_view(k) = LR[i][j].ele[k]; + k_CEclmb.h_view(k) = LR[i][j].CEclmb[k]; } - k_LR.h_view(i,j).k_y.template modify(); - k_LR.h_view(i,j).k_H.template modify(); - k_LR.h_view(i,j).k_vdW.template modify(); - k_LR.h_view(i,j).k_CEvd.template modify(); - k_LR.h_view(i,j).k_ele.template modify(); - k_LR.h_view(i,j).k_CEclmb.template modify(); + k_y.template modify(); + k_H.template modify(); + k_vdW.template modify(); + k_CEvd.template modify(); + k_ele.template modify(); + k_CEclmb.template modify(); - k_LR.h_view(i,j).k_y.template sync(); - k_LR.h_view(i,j).k_H.template sync(); - k_LR.h_view(i,j).k_vdW.template sync(); - k_LR.h_view(i,j).k_CEvd.template sync(); - k_LR.h_view(i,j).k_ele.template sync(); - k_LR.h_view(i,j).k_CEclmb.template sync(); + k_y.template sync(); + k_H.template sync(); + k_vdW.template sync(); + k_CEvd.template sync(); + k_ele.template sync(); + k_CEclmb.template sync(); } } k_LR.template modify(); diff --git a/src/KOKKOS/pair_reax_c_kokkos.h b/src/KOKKOS/pair_reax_c_kokkos.h index 28166df3bd..a6192ed120 100644 --- a/src/KOKKOS/pair_reax_c_kokkos.h +++ b/src/KOKKOS/pair_reax_c_kokkos.h @@ -54,11 +54,6 @@ struct LR_lookup_table_kk double m; double c; - tdual_LR_data_1d k_y; - tdual_cubic_spline_coef_1d k_H; - tdual_cubic_spline_coef_1d k_vdW, k_CEvd; - tdual_cubic_spline_coef_1d k_ele, k_CEclmb; - t_LR_data_1d d_y; t_cubic_spline_coef_1d d_H; t_cubic_spline_coef_1d d_vdW, d_CEvd; @@ -251,8 +246,10 @@ class PairReaxCKokkos : public PairReaxC { void operator()(PairReaxComputeHydrogen, const int&) const; struct params_sing{ + KOKKOS_INLINE_FUNCTION params_sing(){mass=0;chi=0;eta=0;r_s=0;r_pi=0;r_pi2=0;valency=0;valency_val=0;valency_e=0;valency_boc=0;nlp_opt=0; p_lp2=0;p_ovun2=0;p_ovun5=0;p_val3=0;p_val5=0;p_hbond=0;}; + KOKKOS_INLINE_FUNCTION params_sing(int i){mass=0;chi=0;eta=0;r_s=0;r_pi=0;r_pi2=0;valency=0;valency_val=0;valency_e=0;valency_boc=0;nlp_opt=0; p_lp2=0;p_ovun2=0;p_ovun5=0;p_val3=0;p_val5=0;p_hbond=0;}; F_FLOAT mass,chi,eta,r_s,r_pi,r_pi2,valency,valency_val,valency_e,valency_boc,nlp_opt, @@ -260,10 +257,12 @@ class PairReaxCKokkos : public PairReaxC { }; struct params_twbp{ + KOKKOS_INLINE_FUNCTION params_twbp(){gamma=0;gamma_w=0;alpha=0;r_vdw=0;epsilon=0;acore=0;ecore=0;rcore=0;lgre=0;lgcij=0; r_s=0;r_pi=0;r_pi2=0;p_bo1=0;p_bo2=0;p_bo3=0;p_bo4=0;p_bo5=0;p_bo6=0;ovc=0;v13cor=0; p_boc3=0;p_boc4=0;p_boc5=0;p_be1=0,p_be2=0,De_s=0,De_p=0;De_pp=0; p_ovun1=0;}; + KOKKOS_INLINE_FUNCTION params_twbp(int i){gamma=0;gamma_w=0;alpha=0;r_vdw=0;epsilon=0;acore=0;ecore=0;rcore=0;lgre=0;lgcij=0; r_s=0;r_pi=0;r_pi2=0;p_bo1=0;p_bo2=0;p_bo3=0;p_bo4=0;p_bo5=0;p_bo6=0;ovc=0;v13cor=0; p_boc3=0;p_boc4=0;p_boc5=0;p_be1=0,p_be2=0,De_s=0,De_p=0;De_pp=0; @@ -275,19 +274,25 @@ class PairReaxCKokkos : public PairReaxC { }; struct params_thbp{ + KOKKOS_INLINE_FUNCTION params_thbp(){cnt=0;theta_00=0;p_val1=0;p_val2=0;p_val4=0;p_val7=0;p_pen1=0;p_coa1=0;}; + KOKKOS_INLINE_FUNCTION params_thbp(int i){cnt=0;theta_00=0;p_val1=0;p_val2=0;p_val4=0;p_val7=0;p_pen1=0;p_coa1=0;}; F_FLOAT cnt, theta_00, p_val1, p_val2, p_val4, p_val7, p_pen1, p_coa1; }; struct params_fbp{ + KOKKOS_INLINE_FUNCTION params_fbp(){p_tor1=0;p_cot1=0;V1=0;V2=0;V3=0;}; + KOKKOS_INLINE_FUNCTION params_fbp(int i){p_tor1=0;p_cot1=0;V1=0;V2=0;V3=0;}; F_FLOAT p_tor1, p_cot1, V1, V2, V3; }; struct params_hbp{ + KOKKOS_INLINE_FUNCTION params_hbp(){p_hb1=0;p_hb2=0;p_hb3=0;r0_hb=0;}; + KOKKOS_INLINE_FUNCTION params_hbp(int i){p_hb1=0;p_hb2=0;p_hb3=0;r0_hb=0;}; F_FLOAT p_hb1, p_hb2, p_hb3, r0_hb; }; diff --git a/src/MISC/fix_ttm.cpp b/src/MISC/fix_ttm.cpp index f5157139ba..1461a0707d 100644 --- a/src/MISC/fix_ttm.cpp +++ b/src/MISC/fix_ttm.cpp @@ -87,7 +87,8 @@ FixTTM::FixTTM(LAMMPS *lmp, int narg, char **arg) : // error check - if (seed <= 0) error->all(FLERR,"Invalid random number seed in fix ttm command"); + if (seed <= 0) + error->all(FLERR,"Invalid random number seed in fix ttm command"); if (electronic_specific_heat <= 0.0) error->all(FLERR,"Fix ttm electronic_specific_heat must be > 0.0"); if (electronic_density <= 0.0) @@ -342,7 +343,8 @@ void FixTTM::read_initial_electron_temperatures() while (1) { if (fgets(line,MAXLINE,fpr) == NULL) break; sscanf(line,"%d %d %d %lg",&ixnode,&iynode,&iznode,&T_tmp); - if (T_tmp < 0.0) error->one(FLERR,"Fix ttm electron temperatures must be > 0.0"); + if (T_tmp < 0.0) + error->one(FLERR,"Fix ttm electron temperatures must be > 0.0"); T_electron[ixnode][iynode][iznode] = T_tmp; T_initial_set[ixnode][iynode][iznode] = 1; } diff --git a/src/compute_angle_local.cpp b/src/compute_angle_local.cpp index c9d4c00a67..c5478780ae 100644 --- a/src/compute_angle_local.cpp +++ b/src/compute_angle_local.cpp @@ -162,8 +162,8 @@ int ComputeAngleLocal::compute_angles(int flag) atom3 = atom->map(angle_atom3[atom2][i]); } else { if (tag[atom2] != onemols[imol]->angle_atom2[atom2][i]) continue; + atype = onemols[imol]->angle_type[atom2][i]; tagprev = tag[atom2] - iatom - 1; - atype = atom->map(onemols[imol]->angle_type[atom2][i]); atom1 = atom->map(onemols[imol]->angle_atom1[atom2][i]+tagprev); atom3 = atom->map(onemols[imol]->angle_atom3[atom2][i]+tagprev); } diff --git a/src/compute_bond_local.cpp b/src/compute_bond_local.cpp index 6fb1b689b6..7008d81241 100644 --- a/src/compute_bond_local.cpp +++ b/src/compute_bond_local.cpp @@ -156,7 +156,7 @@ int ComputeBondLocal::compute_bonds(int flag) atom2 = atom->map(bond_atom[atom1][i]); } else { tagprev = tag[atom1] - iatom - 1; - btype = atom->map(onemols[imol]->bond_type[iatom][i]); + btype = onemols[imol]->bond_type[iatom][i]; atom2 = atom->map(onemols[imol]->bond_atom[iatom][i]+tagprev); } diff --git a/src/math_extra.h b/src/math_extra.h index 3c00f7a4fc..75dd492845 100644 --- a/src/math_extra.h +++ b/src/math_extra.h @@ -228,7 +228,8 @@ inline void MathExtra::add3(const double *v1, const double *v2, double *ans) ans = s*v1 + v2 ------------------------------------------------------------------------- */ -inline void MathExtra::scaleadd3(double s, const double *v1, const double *v2, double *ans) +inline void MathExtra::scaleadd3(double s, const double *v1, + const double *v2, double *ans) { ans[0] = s*v1[0] + v2[0]; ans[1] = s*v1[1] + v2[1];](_images/sinusoid.jpg){kind=link}