From 03c056ccca7c66534d583deb66a074f974fdd327 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 2 Jul 2007 20:04:44 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@710 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Eqs/Script.create | 1 + doc/Eqs/stress_tensor.jpg | Bin 2657 -> 5078 bytes doc/Eqs/stress_tensor.tex | 3 ++- doc/compute_temp_ramp.html | 2 +- doc/compute_temp_ramp.txt | 2 +- doc/create_atoms.html | 2 +- doc/create_atoms.txt | 2 +- doc/delete_bonds.html | 2 +- doc/delete_bonds.txt | 2 +- doc/displace_atoms.html | 2 +- doc/displace_atoms.txt | 2 +- doc/displace_box.html | 2 +- doc/displace_box.txt | 2 +- doc/dump.html | 39 ++++++++++++++++++++++++------------- doc/dump.txt | 39 ++++++++++++++++++++++++------------- doc/fix_ave_spatial.html | 2 +- doc/fix_ave_spatial.txt | 2 +- doc/fix_deform.html | 2 +- doc/fix_deform.txt | 2 +- doc/fix_indent.html | 4 ++-- doc/fix_indent.txt | 4 ++-- doc/fix_langevin.html | 2 +- doc/fix_langevin.txt | 2 +- doc/fix_momentum.html | 2 +- doc/fix_momentum.txt | 2 +- doc/fix_nph.html | 2 +- doc/fix_nph.txt | 2 +- doc/fix_npt.html | 2 +- doc/fix_npt.txt | 2 +- doc/fix_npt_asphere.html | 2 +- doc/fix_npt_asphere.txt | 2 +- doc/fix_nvt.html | 2 +- doc/fix_nvt.txt | 2 +- doc/fix_nvt_asphere.html | 2 +- doc/fix_nvt_asphere.txt | 2 +- doc/fix_nvt_sllod.html | 2 +- doc/fix_nvt_sllod.txt | 2 +- doc/fix_recenter.html | 2 +- doc/fix_recenter.txt | 2 +- doc/fix_temp_rescale.html | 2 +- doc/fix_temp_rescale.txt | 2 +- doc/fix_viscous.html | 2 +- doc/fix_viscous.txt | 2 +- doc/fix_wall_reflect.html | 2 +- doc/fix_wall_reflect.txt | 2 +- doc/pair_sw.html | 21 ++++++++++---------- doc/pair_sw.txt | 21 ++++++++++---------- doc/region.html | 2 +- doc/region.txt | 2 +- doc/set.html | 2 +- doc/set.txt | 2 +- doc/velocity.html | 2 +- doc/velocity.txt | 2 +- 53 files changed, 121 insertions(+), 99 deletions(-) diff --git a/doc/Eqs/Script.create b/doc/Eqs/Script.create index bbb0c9a62e..ca63e69de4 100755 --- a/doc/Eqs/Script.create +++ b/doc/Eqs/Script.create @@ -26,6 +26,7 @@ latex fix_wall_lj93 latex improper_class2 latex improper_cvff latex improper_harmonic +latex pair_airebo latex pair_buck latex pair_charmm latex pair_class2 diff --git a/doc/Eqs/stress_tensor.jpg b/doc/Eqs/stress_tensor.jpg index 1bd227d9de6e0d3feaea3d4a8a275fe2f8d00bc0..b2516f2f636c904c6297dbc2e335fbd42fa1c0eb 100644 GIT binary patch literal 5078 zcma)gcTf{b^lp$uLX+NDoO z;CKdL3IH(!fk0-^i35Q^r&&0_EGNdr&d$og!^O+X!^OkHCnze!$A4CUheudS_^geYF#`c0p3}Tie5x$`=Zzf&)c!!?D1y=^?zh73W~mE7E_%HD zc1#C=|31+W@OzL1Lm+eiC+Bhu;NEJY%xC3?Cx{dv(KrI#Z#7r4x;Jxb)(FD%LXXS8 z=;_2ACxH@+p~ixkON}aG=(Nr5mok1vio>Rzz!c>Dju zdU?UE_@#~sZt1Z||+B02x?l;8G%r0hf;gFay;Z|dxK;)7;14Kp9iy-2? z{&CVrDOvyC7o~20{fG0H?y<=11@C}rjN95ZT0efIVS^i4MuBdB%t)F32Qx~&=UGSF zok`OKJ7;{9~{6^TG2t8Y^sS+9bXS3>9lM`~HJ7d4g2;b(UkMvtNllA(MU+ws~=- zUXf`m?hjz)i*sY!35}G9CBI~)q#VPt42}1PVppHU&K~+|RXhEsm&*+Kd$fLpSEJ1R z9zVvcsQc)iS0a zu<2s>>?m){j^~dy?oOj1d+KOxv3oBjIVX;&75yr=Op{S2MdX}`>+c?DC42w-P_Fb# z#C&@}WyF$B2&%@?vpK1dgArB5KEXW#qb-msY8u6)Aj}e(g6l)raf!V=wGM>=I+?*ASo>Mx?(Wpz1&GUWO9<+sg@hXTsd*}49=KIL&w+c9m}YK)}H2p ztW*3EPXK3DZ>5C2*l<`vsB8;LBfKF$h7}e7#U*9 zHuhU?zRWf-31Uq%in*scJV8{+TihFP0*`e0bM~nzZVvjAbg+Qbye&B?-Tc1a{J)i$ zbS?1!-;@6(e*w0M$WfBFvbmoQ)S-98Ss=^5XX{F2S_T`D+cs_nUbU%<%b3R-6GNBKW)Z4$Nz#MQXZit2yYCiX0^>DX9~&F2 z&?_g^EEl4czqCnIdr%qYTx7l$9q5{1<1c7lzdJNz zbM5Phh^9;CJ5uwSb%q|b6v$h$8X)I-c^z^}1>_e*Z=X2*;daU=&nLDt#cUFxbR z>53l6-O~@S-?uo?Lh$#UDY_FWxHuRDEQhn=^e$i=*hCX%eTD0WiO=Vy=7|;$gFiK; 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  • vlo,vhi = subtract velocities between vlo and vhi (velocity units)
  • dim = x or y or z
  • clo,chi = lower and upper bound of domain to subtract from (distance units) -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended
  • keyword = units 
      units value = lattice or box 
diff --git a/doc/compute_temp_ramp.txt b/doc/compute_temp_ramp.txt
index b0345bebc8..2ba575201e 100644
--- a/doc/compute_temp_ramp.txt
+++ b/doc/compute_temp_ramp.txt
@@ -18,7 +18,7 @@ vdim = {vx} or {vy} or {vz}
 vlo,vhi = subtract velocities between vlo and vhi (velocity units)
 dim = {x} or {y} or {z}
 clo,chi = lower and upper bound of domain to subtract from (distance units)
-zero or more keyword/value pairs may be appended to the args
+zero or more keyword/value pairs may be appended
 keyword = {units} :ul
   {units} value = {lattice} or {box} :pre
 
diff --git a/doc/create_atoms.html b/doc/create_atoms.html
index 139b6d5b7f..f28c670f5d 100644
--- a/doc/create_atoms.html
+++ b/doc/create_atoms.html
@@ -25,7 +25,7 @@
   single args = x y z
     x,y,z = coordinates of a single atom (distance units)
    -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended
  • keyword = basis or units diff --git a/doc/create_atoms.txt b/doc/create_atoms.txt index 654cde0900..58671d2611 100644 --- a/doc/create_atoms.txt +++ b/doc/create_atoms.txt @@ -19,7 +19,7 @@ style = {box} or {region} or {single} :l region-ID = atoms will only be created if contained in the region {single} args = x y z x,y,z = coordinates of a single atom (distance units) :pre -zero or more keyword/value pairs may be appended to the args :l +zero or more keyword/value pairs may be appended :l keyword = {basis} or {units} :l {basis} values = M itype M = which basis atom diff --git a/doc/delete_bonds.html b/doc/delete_bonds.html index 3a685c11a7..9db79de558 100644 --- a/doc/delete_bonds.html +++ b/doc/delete_bonds.html @@ -28,7 +28,7 @@ improper args = an improper type stats args = none -
  • zero or more keywords may be appended to the args +
  • zero or more keywords may be appended
  • keyword = undo or remove or special diff --git a/doc/delete_bonds.txt b/doc/delete_bonds.txt index c116fb6a8e..cb81cae4ef 100644 --- a/doc/delete_bonds.txt +++ b/doc/delete_bonds.txt @@ -22,7 +22,7 @@ style = {multi} or {atom} or {bond} or {angle} or {dihedral} or {dihedral} args = a dihedral type {improper} args = an improper type {stats} args = none :pre -zero or more keywords may be appended to the args :l +zero or more keywords may be appended :l keyword = {undo} or {remove} or {special} :l :ule diff --git a/doc/displace_atoms.html b/doc/displace_atoms.html index 2ae031f132..c2918fb626 100644 --- a/doc/displace_atoms.html +++ b/doc/displace_atoms.html @@ -30,7 +30,7 @@ dx,dy,dz = random displacement magnitude in each dimension (distance units) seed = random # seed (8 digits or less) -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended 
      keyword = units
     value = box or lattice 
diff --git a/doc/displace_atoms.txt b/doc/displace_atoms.txt
index 26fa1672c4..0758f5d56a 100644
--- a/doc/displace_atoms.txt
+++ b/doc/displace_atoms.txt
@@ -24,7 +24,7 @@ style = {move} or {ramp} or {random} :l
   {random} args = dx dy dz seed
     dx,dy,dz = random displacement magnitude in each dimension (distance units)
     seed = random # seed (8 digits or less) :pre
-zero or more keyword/value pairs may be appended to the args :l
+zero or more keyword/value pairs may be appended :l
   keyword = {units}
     value = {box} or {lattice} :pre
 :ule
diff --git a/doc/displace_box.html b/doc/displace_box.html
index 520bba37f5..8ca06c2f4b 100644
--- a/doc/displace_box.html
+++ b/doc/displace_box.html
@@ -36,7 +36,7 @@
       delta value = dtilt
         dtilt = change in tilt factor at end of run (distance units)
    -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended
  • keyword = remap or units diff --git a/doc/displace_box.txt b/doc/displace_box.txt index 9ce44994eb..069c05c72e 100644 --- a/doc/displace_box.txt +++ b/doc/displace_box.txt @@ -31,7 +31,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz} {delta} value = dtilt dtilt = change in tilt factor at end of run (distance units) :pre -zero or more keyword/value pairs may be appended to the args :l +zero or more keyword/value pairs may be appended :l keyword = {remap} or {units} :l {remap} value = {x} or {none} x = remap coords of atoms in group into deforming box diff --git a/doc/dump.html b/doc/dump.html index 2a24b7b333..17458fb1dd 100644 --- a/doc/dump.html +++ b/doc/dump.html @@ -39,7 +39,7 @@ vx, vy, vz, fx, fy, fz, q, mux, muy, muz, quatw, quati, quatj, quatk, tqx, tqy, tqz, - epair, ke, etotal, centro, + epair, ebond, ke, etotal, centro, sxx, syy, szz, sxy, sxz, syz, c_ID, c_ID[N] tag = atom ID @@ -56,8 +56,9 @@ quatw,quati,quatj,quatk = quaternion components for aspherical particles tqx,tqy,tqz = torque on aspherical particles epair = per-atom pairwise energy + epair = per-atom bond energy ke = per-atom kinetic energy - etotal = per-atom total energy (ke + epair) + etotal = per-atom total energy (ke + epair, not ebond) centro = per-atom centro-symmetry parameter sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components c_ID = scalar per-atom quantity calculated by a compute identified by its ID @@ -240,15 +241,17 @@ are specific to aspherical particles defined with an atom style of define the orientiation of the particle. The final 3 give the rotational torque on the particle.

    -

    The epair, ke, etotal, centro, and sxx, etc keywords print -the pairwise energy, kinetic energy, total energy (pairwise + -kinetic), centro-symmetry parameter, and components of the per-atom -stress tensor for each atom. These quantities are calculated by -computes that the dump defines, as if these commands had been issued: +

    The epair, ebond, ke, etotal, centro, and sxx, etc +keywords print the pairwise energy, bond energy, kinetic energy, total +energy (pairwise + kinetic), centro-symmetry parameter, and components +of the per-atom stress tensor for each atom. These quantities are +calculated by computes that the dump defines, as if these commands had +been issued: 

    compute dump-ID_epair/atom group-ID epair/atom
+compute dump-ID_ebond/atom group-ID ebond/atom
 compute dump-ID_ke/atom group-ID ke/atom
-compute dump-ID_etotal/atom group-ID etotal/atom
+compute dump-ID_etotal/atom group-ID etotal/atom dump-ID_epair/atom
 compute dump-ID_centro/atom group-ID centro/atom
 compute dump-ID_stress/atom group-ID stress/atom
    @@ -256,10 +259,16 @@ compute dump-ID_stress/atom group-ID stress details on what is computed for each atom. Note that the ID of each new compute is the dump-ID with the compute style appended (with an underscore). The group for each new compute is the same as the dump -group. +group. Note that for etotal, an auxiliary compute for calculating +the pairwise energy is created, since the compute +etotal/atom command requires it as an extra +argument.

    -

    Note that the etotal keyword does not include energy contributions -due to bonds, angles, etc that the atom is part of. +

    IMPORTANT NOTE: The etotal keyword does NOT include contributions +due to bonds, angles, etc that the atom is part of. The bond +contribution can be computed separately via the ebond keyword. +Currently, there is no way in LAMMPS to dump per-atom energy for +angles, dihedrals, improper, or long-range interactions.

    The sxx, syy, szz, sxy, sxz, syz keywords access the 6 components of the stress tensor calculated for each atom by the @@ -311,9 +320,11 @@ files are written with, which will result in a compile-time error when a lo-level include file is not found. Putting this style in a package makes it easy to exclude from a LAMMPS build for those machines.

    -

    Granular systems and granular pair potentials cannot be used to -compute per-atom energy and stress. The fix -gran/diag command should be used instead. +

    Some pair potentials do not allow the calculation of per-atom energy +and stress via the epair, etotal, sxx, etc keywords. One of +these are the granular pair potentials. However, for those +potentials, the fix gran/diag command can be used +instead.

    Related commands:

    diff --git a/doc/dump.txt b/doc/dump.txt index 965d7453f5..d5880deb1f 100644 --- a/doc/dump.txt +++ b/doc/dump.txt @@ -30,7 +30,7 @@ args = list of arguments for a particular style :l vx, vy, vz, fx, fy, fz, q, mux, muy, muz, quatw, quati, quatj, quatk, tqx, tqy, tqz, - epair, ke, etotal, centro, + epair, ebond, ke, etotal, centro, sxx, syy, szz, sxy, sxz, syz, c_ID, c_ID\[N\] tag = atom ID @@ -47,8 +47,9 @@ args = list of arguments for a particular style :l quatw,quati,quatj,quatk = quaternion components for aspherical particles tqx,tqy,tqz = torque on aspherical particles epair = per-atom pairwise energy + epair = per-atom bond energy ke = per-atom kinetic energy - etotal = per-atom total energy (ke + epair) + etotal = per-atom total energy (ke + epair, not ebond) centro = per-atom centro-symmetry parameter sxx, syy, szz, sxy, sxz, syz = per-atom stress tensor components c_ID = scalar per-atom quantity calculated by a compute identified by its ID @@ -230,15 +231,17 @@ are specific to aspherical particles defined with an atom style of define the orientiation of the particle. The final 3 give the rotational torque on the particle. -The {epair}, {ke}, {etotal}, {centro}, and {sxx}, etc keywords print -the pairwise energy, kinetic energy, total energy (pairwise + -kinetic), centro-symmetry parameter, and components of the per-atom -stress tensor for each atom. These quantities are calculated by -computes that the dump defines, as if these commands had been issued: +The {epair}, {ebond}, {ke}, {etotal}, {centro}, and {sxx}, etc +keywords print the pairwise energy, bond energy, kinetic energy, total +energy (pairwise + kinetic), centro-symmetry parameter, and components +of the per-atom stress tensor for each atom. These quantities are +calculated by computes that the dump defines, as if these commands had +been issued: compute dump-ID_epair/atom group-ID "epair/atom"_compute_epair_atom.html +compute dump-ID_ebond/atom group-ID "ebond/atom"_compute_ebond_atom.html compute dump-ID_ke/atom group-ID "ke/atom"_compute_ke_atom.html -compute dump-ID_etotal/atom group-ID "etotal/atom"_compute_etotal_atom.html +compute dump-ID_etotal/atom group-ID "etotal/atom"_compute_etotal_atom.html dump-ID_epair/atom compute dump-ID_centro/atom group-ID "centro/atom"_compute_centro_atom.html compute dump-ID_stress/atom group-ID "stress/atom"_compute_stress_atom.html :pre @@ -246,10 +249,16 @@ See the corresponding "compute"_compute.html style commands for details on what is computed for each atom. Note that the ID of each new compute is the dump-ID with the compute style appended (with an underscore). The group for each new compute is the same as the dump -group. +group. Note that for {etotal}, an auxiliary compute for calculating +the pairwise energy is created, since the "compute +etotal/atom"_compute_etotal_atom.html command requires it as an extra +argument. -Note that the {etotal} keyword does not include energy contributions -due to bonds, angles, etc that the atom is part of. +IMPORTANT NOTE: The {etotal} keyword does NOT include contributions +due to bonds, angles, etc that the atom is part of. The bond +contribution can be computed separately via the {ebond} keyword. +Currently, there is no way in LAMMPS to dump per-atom energy for +angles, dihedrals, improper, or long-range interactions. The {sxx}, {syy}, {szz}, {sxy}, {sxz}, {syz} keywords access the 6 components of the stress tensor calculated for each atom by the @@ -301,9 +310,11 @@ files are written with, which will result in a compile-time error when a lo-level include file is not found. Putting this style in a package makes it easy to exclude from a LAMMPS build for those machines. -Granular systems and granular pair potentials cannot be used to -compute per-atom energy and stress. The "fix -gran/diag"_fix_gran_diag.html command should be used instead. +Some pair potentials do not allow the calculation of per-atom energy +and stress via the {epair}, {etotal}, {sxx}, etc keywords. One of +these are the granular pair potentials. However, for those +potentials, the "fix gran/diag"_fix_gran_diag.html command can be used +instead. [Related commands:] diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html index cabe01dce3..6af3435195 100644 --- a/doc/fix_ave_spatial.html +++ b/doc/fix_ave_spatial.html @@ -39,7 +39,7 @@ atom arg = vx or vy or vz or fx or fy or fz compute arg = compute-ID that calculates per-atom quantities -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended 
    keyword = norm or units
   norm value = all or sample
diff --git a/doc/fix_ave_spatial.txt b/doc/fix_ave_spatial.txt
index c07e229c08..7f02d27dd2 100644
--- a/doc/fix_ave_spatial.txt
+++ b/doc/fix_ave_spatial.txt
@@ -27,7 +27,7 @@ style = {density} or {atom} or {compute} :l
   {atom} arg = {vx} or {vy} or {vz} or {fx} or {fy} or {fz}
   {compute} arg = compute-ID that calculates per-atom quantities :pre
 
-zero or more keyword/value pairs may be appended to the args :l
+zero or more keyword/value pairs may be appended :l
 keyword = {norm} or {units}
   {norm} value = {all} or {sample}
   {units} value = {box} or {lattice} or {reduced} :pre
diff --git a/doc/fix_deform.html b/doc/fix_deform.html
index 4db3509281..7ab2cceccd 100644
--- a/doc/fix_deform.html
+++ b/doc/fix_deform.html
@@ -55,7 +55,7 @@
 
          trate value = R
         R = true shear strain rate (1/time units) 
 
    
-
  • zero or more keyword/value pairs may be appended to the args 
+
  • zero or more keyword/value pairs may be appended 
 
 
  • keyword = remap or units 
 
diff --git a/doc/fix_deform.txt b/doc/fix_deform.txt
index d1e8e6de83..e0ff031fb0 100644
--- a/doc/fix_deform.txt
+++ b/doc/fix_deform.txt
@@ -47,7 +47,7 @@ parameter = {x} or {y} or {z} or {xy} or {xz} or {yz}
       {trate} value = R
         R = true shear strain rate (1/time units) :pre
 
-zero or more keyword/value pairs may be appended to the args :l
+zero or more keyword/value pairs may be appended :l
 keyword = {remap} or {units} :l
   {remap} value = {x} or {v} or {none}
     x = remap coords of atoms in group into deforming box
diff --git a/doc/fix_indent.html b/doc/fix_indent.html
index d66cd11c6a..4ed98e394d 100644
--- a/doc/fix_indent.html
+++ b/doc/fix_indent.html
@@ -13,7 +13,7 @@
 
 
    Syntax:
 
    
-
    fix ID group-ID indent k keyword args ... 
+
    fix ID group-ID indent k keyword values ... 
 
    
 
    • ID, group-ID are documented in fix command 
 
@@ -21,7 +21,7 @@
 
 
    • k = force constant for indenter surface (force/distance^2 units) 
 
-
    • one or more keyword/value pairs may be appended to the args 
+
    • one or more keyword/value pairs may be appended 
 
 
    • keyword = sphere or cylinder or vel or rstart or units 
 
diff --git a/doc/fix_indent.txt b/doc/fix_indent.txt
index 50947370e7..c22eeb9c0f 100644
--- a/doc/fix_indent.txt
+++ b/doc/fix_indent.txt
@@ -10,12 +10,12 @@ fix indent command :h3
 
 [Syntax:]
 
-fix ID group-ID indent k keyword args ... :pre
+fix ID group-ID indent k keyword values ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 indent = style name of this fix command :l
 k = force constant for indenter surface (force/distance^2 units) :l
-one or more keyword/value pairs may be appended to the args :l
+one or more keyword/value pairs may be appended :l
 keyword = {sphere} or {cylinder} or {vel} or {rstart} or {units} :l
   {sphere} args = x y z R
     x,y,z = initial position of center of indenter
diff --git a/doc/fix_langevin.html b/doc/fix_langevin.html
index ba0ccdf5de..04fb73a6b7 100644
--- a/doc/fix_langevin.html
+++ b/doc/fix_langevin.html
@@ -25,7 +25,7 @@
 
 
    • seed = random # seed to use for white noise (8 digits or less) 
 
-
    • zero or more keyword/value pairs may be appended to the args 
+
    • zero or more keyword/value pairs may be appended 
 
 
      keyword = axes or scale or region
   axes values = xflag yflag zflag
diff --git a/doc/fix_langevin.txt b/doc/fix_langevin.txt
index 869649c609..7d400c9fe1 100644
--- a/doc/fix_langevin.txt
+++ b/doc/fix_langevin.txt
@@ -17,7 +17,7 @@ langevin = style name of this fix command :l
 Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
 damp = damping parameter (time units) :l
 seed = random # seed to use for white noise (8 digits or less) :l
-zero or more keyword/value pairs may be appended to the args :l
+zero or more keyword/value pairs may be appended :l
 keyword = {axes} or {scale} or {region}
   {axes} values = xflag yflag zflag
     xflag,yflag,zflag = 0/1 to exclude/include a dimension in the thermostat
diff --git a/doc/fix_momentum.html b/doc/fix_momentum.html
index 89d7eb6f8a..86da567691 100644
--- a/doc/fix_momentum.html
+++ b/doc/fix_momentum.html
@@ -20,7 +20,7 @@
 
    • momentum = style name of this fix command 
 
 
    • N = adjust the momentum every this many timesteps
-one or more keyword/value pairs may be appended to the args 
+one or more keyword/value pairs may be appended 
 
 
    • keyword = linear or angular 
 
diff --git a/doc/fix_momentum.txt b/doc/fix_momentum.txt
index 8a1c3ed983..3ae5ff2091 100644
--- a/doc/fix_momentum.txt
+++ b/doc/fix_momentum.txt
@@ -15,7 +15,7 @@ fix ID group-ID momentum N keyword values ... :pre
 ID, group-ID are documented in "fix"_fix.html command :ulb,l
 momentum = style name of this fix command :l
 N = adjust the momentum every this many timesteps
-one or more keyword/value pairs may be appended to the args :l
+one or more keyword/value pairs may be appended :l
 keyword = {linear} or {angular} :l
   {linear} values = xflag yflag zflag
     xflag,yflag,zflag = 0/1 to exclude/include each dimension
diff --git a/doc/fix_nph.html b/doc/fix_nph.html
index 4cb1ebbfa6..8c7cc9328a 100644
--- a/doc/fix_nph.html
+++ b/doc/fix_nph.html
@@ -33,7 +33,7 @@
       start/end (0/1) of run (pressure units)
     Pdamp = pressure damping parameter (time units) 
 
      • 
-
    • zero or more keyword/value pairs may be appended to the args 
+
    • zero or more keyword/value pairs may be appended 
 
 
    • keyword = drag or dilate 
 
diff --git a/doc/fix_nph.txt b/doc/fix_nph.txt
index 01a34c7fb2..7e94babce0 100644
--- a/doc/fix_nph.txt
+++ b/doc/fix_nph.txt
@@ -27,7 +27,7 @@ p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
       start/end (0/1) of run (pressure units)
     Pdamp = pressure damping parameter (time units) :pre
 
-zero or more keyword/value pairs may be appended to the args :l
+zero or more keyword/value pairs may be appended :l
 keyword = {drag} or {dilate} :l
   {drag} value = drag factor added to barostat (0.0 = no drag)
   {dilate} value = {all} or {partial} :pre
diff --git a/doc/fix_npt.html b/doc/fix_npt.html
index f765d33167..140f0883fd 100644
--- a/doc/fix_npt.html
+++ b/doc/fix_npt.html
@@ -32,7 +32,7 @@
     Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
     Pdamp = pressure damping parameter (time units) 
 
    
-
  • zero or more keyword/value pairs may be appended to the args 
+
  • zero or more keyword/value pairs may be appended 
 
 
  • keyword = drag or dilate 
 
diff --git a/doc/fix_npt.txt b/doc/fix_npt.txt
index 00e4aa87b1..23fc1c8908 100644
--- a/doc/fix_npt.txt
+++ b/doc/fix_npt.txt
@@ -24,7 +24,7 @@ p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l
     Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
     Pdamp = pressure damping parameter (time units) :pre
 
-zero or more keyword/value pairs may be appended to the args :l
+zero or more keyword/value pairs may be appended :l
 keyword = {drag} or {dilate} :l
   {drag} value = drag factor added to barostat/thermostat (0.0 = no drag)
   {dilate} value = {all} or {partial} :pre
diff --git a/doc/fix_npt_asphere.html b/doc/fix_npt_asphere.html
index d91d02aa87..c2a129e00b 100644
--- a/doc/fix_npt_asphere.html
+++ b/doc/fix_npt_asphere.html
@@ -32,7 +32,7 @@
     Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
     Pdamp = pressure damping parameter (time units)
    • -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended
  • keyword = drag or dilate diff --git a/doc/fix_npt_asphere.txt b/doc/fix_npt_asphere.txt index 0661677692..87afd896dc 100755 --- a/doc/fix_npt_asphere.txt +++ b/doc/fix_npt_asphere.txt @@ -24,7 +24,7 @@ p-style = {xyz} or {xy} or {yz} or {xz} or {aniso} :l Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units) Pdamp = pressure damping parameter (time units) :pre -zero or more keyword/value pairs may be appended to the args :l +zero or more keyword/value pairs may be appended :l keyword = {drag} or {dilate} :l {drag} value = drag factor added to barostat/thermostat (0.0 = no drag) {dilate} value = {all} or {partial} :pre diff --git a/doc/fix_nvt.html b/doc/fix_nvt.html index a1939a03d7..2238ac8095 100644 --- a/doc/fix_nvt.html +++ b/doc/fix_nvt.html @@ -23,7 +23,7 @@
  • Tdamp = temperature damping parameter (time units) -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended
  • keyword = drag diff --git a/doc/fix_nvt.txt b/doc/fix_nvt.txt index b50df05e0c..08350114f1 100644 --- a/doc/fix_nvt.txt +++ b/doc/fix_nvt.txt @@ -17,7 +17,7 @@ nvt = style name of this fix command :l Tstart,Tstop = desired temperature at start/end of run :l Tdamp = temperature damping parameter (time units) :l -zero or more keyword/value pairs may be appended to the args :l +zero or more keyword/value pairs may be appended :l keyword = {drag} :l {drag} value = drag factor added to thermostat (0.0 = no drag) :pre :ule diff --git a/doc/fix_nvt_asphere.html b/doc/fix_nvt_asphere.html index cdffdedb76..5da14c27bc 100644 --- a/doc/fix_nvt_asphere.html +++ b/doc/fix_nvt_asphere.html @@ -23,7 +23,7 @@
  • Tdamp = temperature damping parameter (time units) -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended
  • keyword = drag diff --git a/doc/fix_nvt_asphere.txt b/doc/fix_nvt_asphere.txt index e38b3ba717..84343089a1 100755 --- a/doc/fix_nvt_asphere.txt +++ b/doc/fix_nvt_asphere.txt @@ -17,7 +17,7 @@ nvt/asphere = style name of this fix command :l Tstart,Tstop = desired temperature at start/end of run :l Tdamp = temperature damping parameter (time units) :l -zero or more keyword/value pairs may be appended to the args :l +zero or more keyword/value pairs may be appended :l keyword = {drag} :l {drag} value = drag factor added to thermostat (0.0 = no drag) :pre :ule diff --git a/doc/fix_nvt_sllod.html b/doc/fix_nvt_sllod.html index 1ee4502548..493b6afbb8 100644 --- a/doc/fix_nvt_sllod.html +++ b/doc/fix_nvt_sllod.html @@ -23,7 +23,7 @@
  • Tdamp = temperature damping parameter (time units) -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended
  • keyword = drag diff --git a/doc/fix_nvt_sllod.txt b/doc/fix_nvt_sllod.txt index f951f8c112..8bbf55a4e1 100644 --- a/doc/fix_nvt_sllod.txt +++ b/doc/fix_nvt_sllod.txt @@ -17,7 +17,7 @@ nvt/sllod = style name of this fix command :l Tstart,Tstop = desired temperature at start/end of run :l Tdamp = temperature damping parameter (time units) :l -zero or more keyword/value pairs may be appended to the args :l +zero or more keyword/value pairs may be appended :l keyword = {drag} :l {drag} value = drag factor added to thermostat (0.0 = no drag) :pre :ule diff --git a/doc/fix_recenter.html b/doc/fix_recenter.html index c467b29207..ee09c1cf0d 100644 --- a/doc/fix_recenter.html +++ b/doc/fix_recenter.html @@ -21,7 +21,7 @@
  • x,y,z = constrain center-of-mass to these coords (distance units), any coord can also be NULL or INIT (see below) -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended
  • keyword = shift or units diff --git a/doc/fix_recenter.txt b/doc/fix_recenter.txt index a9d7809208..c093bd2ca7 100644 --- a/doc/fix_recenter.txt +++ b/doc/fix_recenter.txt @@ -16,7 +16,7 @@ ID, group-ID are documented in "fix"_fix.html command :ulb,l recenter = style name of this fix command :l x,y,z = constrain center-of-mass to these coords (distance units), \ any coord can also be NULL or INIT (see below) :l -zero or more keyword/value pairs may be appended to the args :l +zero or more keyword/value pairs may be appended :l keyword = {shift} or {units} :l {shift} value = group-ID group-ID = group of atoms whose coords are shifted diff --git a/doc/fix_temp_rescale.html b/doc/fix_temp_rescale.html index 7f84d702fe..ea36b7045a 100644 --- a/doc/fix_temp_rescale.html +++ b/doc/fix_temp_rescale.html @@ -21,7 +21,7 @@
  • Tstart,Tstop = desired temperature at start/end of run (temperature units)
  • window = only rescale if temperature is outside this window (temperature units)
  • fraction = rescale to target temperature by this fraction -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended
  • keyword = region 
      region values = region-ID of region to apply rescaling to 
diff --git a/doc/fix_temp_rescale.txt b/doc/fix_temp_rescale.txt
index 9ae3d08d62..0b294cb474 100644
--- a/doc/fix_temp_rescale.txt
+++ b/doc/fix_temp_rescale.txt
@@ -18,7 +18,7 @@ N = perform rescaling every N steps
 Tstart,Tstop = desired temperature at start/end of run (temperature units)
 window = only rescale if temperature is outside this window (temperature units)
 fraction = rescale to target temperature by this fraction
-zero or more keyword/value pairs may be appended to the args
+zero or more keyword/value pairs may be appended
 keyword = {region} :ul
   {region} values = region-ID of region to apply rescaling to :pre
 
diff --git a/doc/fix_viscous.html b/doc/fix_viscous.html
index c536a974e9..97b559dba4 100644
--- a/doc/fix_viscous.html
+++ b/doc/fix_viscous.html
@@ -25,7 +25,7 @@
 
 
  • keyword = b or a or t or m 
 
-
  • zero or more keyword/value pairs may be appended to the args 
+
  • zero or more keyword/value pairs may be appended 
 
 
    keyword = scale
   scale values = type ratio
diff --git a/doc/fix_viscous.txt b/doc/fix_viscous.txt
index bec27a7054..9a9f8a517a 100644
--- a/doc/fix_viscous.txt
+++ b/doc/fix_viscous.txt
@@ -17,7 +17,7 @@ viscous = style name of this fix command :l
 gamma = damping coefficient (force/velocity units) :l
 zero or more keyword/value pairs can be appended :l
 keyword = {b} or {a} or {t} or {m} :l
-zero or more keyword/value pairs may be appended to the args :l
+zero or more keyword/value pairs may be appended :l
 keyword = {scale}
   {scale} values = type ratio
     type = atom type (1-N)
diff --git a/doc/fix_wall_reflect.html b/doc/fix_wall_reflect.html
index 85c644b02c..f507974741 100644
--- a/doc/fix_wall_reflect.html
+++ b/doc/fix_wall_reflect.html
@@ -17,7 +17,7 @@
 
    
 
    • ID, group-ID are documented in fix command
 
    • wall/reflect = style name of this fix command
-
    • one or more keyword/value pairs may be appended to the args
+
    • one or more keyword/value pairs may be appended
 
    • keyword = xlo or xhi or ylo or yhi or zlo or zhi 
 
    
 
    Examples:
diff --git a/doc/fix_wall_reflect.txt b/doc/fix_wall_reflect.txt
index 334a3229ea..1d2d48cdeb 100644
--- a/doc/fix_wall_reflect.txt
+++ b/doc/fix_wall_reflect.txt
@@ -14,7 +14,7 @@ fix ID group-ID wall/reflect keyword ... :pre
 
 ID, group-ID are documented in "fix"_fix.html command
 wall/reflect = style name of this fix command
-one or more keyword/value pairs may be appended to the args
+one or more keyword/value pairs may be appended
 keyword = {xlo} or {xhi} or {ylo} or {yhi} or {zlo} or {zhi} :ul
 
 [Examples:]
diff --git a/doc/pair_sw.html b/doc/pair_sw.html
index b33623832b..c1a82440e1 100644
--- a/doc/pair_sw.html
+++ b/doc/pair_sw.html
@@ -98,17 +98,16 @@ entries would be required, etc.
 
    As annotated above, the first element in the entry is the center atom
 in a three-body interaction.  Thus an entry for SiCC means a Si atom
 with 2 C atoms as neighbors.  By symmetry, three-body parameters for
-SiCSi and SiSiC entries should be the same.   The parameters used for 
-the two-body interaction come
-from the entry where the 2nd element is repeated.  Thus the two-body
-parameters for Si interacting with C, comes from the SiCC entry.  
-Again by symmetry, the two-body parameters in the SiCC
-and CSiSi entries should thus be the same. 
-The parameters used for a particular three-body 
-interaction come from the entry with the corresponding three elements. 
-The parameters used only for two-body interactions (A, B, p, and q) 
-in entries whose 2nd and 3rd element are different (e.g. SiCSi) 
-are not used for anything and can be set to 0.0 if desired.
+SiCSi and SiSiC entries should be the same.  The parameters used for
+the two-body interaction come from the entry where the 2nd element is
+repeated.  Thus the two-body parameters for Si interacting with C,
+comes from the SiCC entry.  Again by symmetry, the two-body parameters
+in the SiCC and CSiSi entries should thus be the same.  The parameters
+used for a particular three-body interaction come from the entry with
+the corresponding three elements.  The parameters used only for
+two-body interactions (A, B, p, and q) in entries whose 2nd and 3rd
+element are different (e.g. SiCSi) are not used for anything and can
+be set to 0.0 if desired.
 
    
 
    
 
diff --git a/doc/pair_sw.txt b/doc/pair_sw.txt
index 3797815995..58afab3b0f 100644
--- a/doc/pair_sw.txt
+++ b/doc/pair_sw.txt
@@ -95,17 +95,16 @@ entries would be required, etc.
 As annotated above, the first element in the entry is the center atom
 in a three-body interaction.  Thus an entry for SiCC means a Si atom
 with 2 C atoms as neighbors.  By symmetry, three-body parameters for
-SiCSi and SiSiC entries should be the same.   The parameters used for 
-the two-body interaction come
-from the entry where the 2nd element is repeated.  Thus the two-body
-parameters for Si interacting with C, comes from the SiCC entry.  
-Again by symmetry, the two-body parameters in the SiCC
-and CSiSi entries should thus be the same. 
-The parameters used for a particular three-body 
-interaction come from the entry with the corresponding three elements. 
-The parameters used only for two-body interactions (A, B, p, and q) 
-in entries whose 2nd and 3rd element are different (e.g. SiCSi) 
-are not used for anything and can be set to 0.0 if desired.
+SiCSi and SiSiC entries should be the same.  The parameters used for
+the two-body interaction come from the entry where the 2nd element is
+repeated.  Thus the two-body parameters for Si interacting with C,
+comes from the SiCC entry.  Again by symmetry, the two-body parameters
+in the SiCC and CSiSi entries should thus be the same.  The parameters
+used for a particular three-body interaction come from the entry with
+the corresponding three elements.  The parameters used only for
+two-body interactions (A, B, p, and q) in entries whose 2nd and 3rd
+element are different (e.g. SiCSi) are not used for anything and can
+be set to 0.0 if desired.
 
 :line
 
diff --git a/doc/region.html b/doc/region.html
index 3bf6b17890..aaa0ba01ad 100644
--- a/doc/region.html
+++ b/doc/region.html
@@ -42,7 +42,7 @@
     N = # of regions to follow, must be 2 or greater
     reg-ID1,reg-ID2, ... = IDs of regions to intersect
    • -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended
  • keyword = side or units diff --git a/doc/region.txt b/doc/region.txt index 48feb323df..6ae9ef7cb8 100644 --- a/doc/region.txt +++ b/doc/region.txt @@ -36,7 +36,7 @@ style = {block} or {cylinder} or {prism} or {sphere} or {union} or {intersect} : {intersect} args = N reg-ID1 reg-ID2 ... N = # of regions to follow, must be 2 or greater reg-ID1,reg-ID2, ... = IDs of regions to intersect :pre -zero or more keyword/value pairs may be appended to the args :l +zero or more keyword/value pairs may be appended :l keyword = {side} or {units} :l {side} value = {in} or {out} {in} = the region is inside the specified geometry diff --git a/doc/set.html b/doc/set.html index 93d1f85919..27b29b35c3 100644 --- a/doc/set.html +++ b/doc/set.html @@ -19,7 +19,7 @@
  • ID = atom ID or group ID or region ID -
  • one or more keyword/value pairs may be appended to the args +
  • one or more keyword/value pairs may be appended
  • keyword = type or type/fraction or mol or x or y or z or vx or vy or vz or charge or dipole or dipole/random or quat/random or bond or angle or dihedral or improper diff --git a/doc/set.txt b/doc/set.txt index b3c011374a..e3aabf238a 100644 --- a/doc/set.txt +++ b/doc/set.txt @@ -14,7 +14,7 @@ set style ID keyword value ... :pre style = {atom} or {group} or {region} :ulb,l ID = atom ID or group ID or region ID :l -one or more keyword/value pairs may be appended to the args :l +one or more keyword/value pairs may be appended :l keyword = {type} or {type/fraction} or {mol} or \ {x} or {y} or {z} or {vx} or {vy} or {vz} or \ {charge} or {dipole} or {dipole/random} or {quat/random} or \ diff --git a/doc/velocity.html b/doc/velocity.html index 072ce98f93..4a2909c0d6 100644 --- a/doc/velocity.html +++ b/doc/velocity.html @@ -35,7 +35,7 @@ linear = zero the linear momentum angular = zero the angular momentum -
  • zero or more keyword/value pairs may be appended to the args +
  • zero or more keyword/value pairs may be appended
  • keyword = dist or sum or mom or rot or temp or loop or units diff --git a/doc/velocity.txt b/doc/velocity.txt index a548e33797..3d0a053577 100644 --- a/doc/velocity.txt +++ b/doc/velocity.txt @@ -30,7 +30,7 @@ style = {create} or {set} or {scale} or {ramp} or {zero} :l {linear} = zero the linear momentum {angular} = zero the angular momentum :pre -zero or more keyword/value pairs may be appended to the args :l +zero or more keyword/value pairs may be appended :l keyword = {dist} or {sum} or {mom} or {rot} or {temp} or {loop} or {units} :l {dist} value = {uniform} or {gaussian} {sum} value = {no} or {yes}