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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2332 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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20
doc/Section_commands.html
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@ -113,8 +113,8 @@ line are arguments.
<P>(6) Text with spaces can be enclosed in double quotes so it will be <P>(6) Text with spaces can be enclosed in double quotes so it will be
treated as a single argument. See the <A HREF = "dump_modify.html">dump modify</A> treated as a single argument. See the <A HREF = "dump_modify.html">dump modify</A>
or <A HREF = "fix_print.html">fix print</A> commands for examples. A '#' or '$' or <A HREF = "fix_print.html">fix print</A> commands for examples. A '#' or '$'
character that in text between double quotes will not be treated as a character that is in text between double quotes will not be treated as
comment or substituted for as a variable. a comment or substituted for as a variable.
</P> </P>
<HR> <HR>
@ -317,14 +317,14 @@ in the command's documentation.
of each style or click on the style itself for a full description: of each style or click on the style itself for a full description:
</P> </P>
<DIV ALIGN=center><TABLE BORDER=1 > <DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_coord_original.html">coord/original</A></TD></TR> <TR ALIGN="center"><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD></TR> <TR ALIGN="center"><TD ><A HREF = "fix_com.html">com</A></TD><TD ><A HREF = "fix_coord_original.html">coord/original</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD></TR> <TR ALIGN="center"><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_gyration.html">gyration</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD></TR> <TR ALIGN="center"><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD></TR> <TR ALIGN="center"><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD></TR> <TR ALIGN="center"><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD></TR> <TR ALIGN="center"><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A> <TR ALIGN="center"><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV> </TD></TR></TABLE></DIV>
<P>These are fix styles contributed by users, which can be used if <P>These are fix styles contributed by users, which can be used if

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doc/Section_commands.txt
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@ -110,8 +110,8 @@ line are arguments.
(6) Text with spaces can be enclosed in double quotes so it will be (6) Text with spaces can be enclosed in double quotes so it will be
treated as a single argument. See the "dump modify"_dump_modify.html treated as a single argument. See the "dump modify"_dump_modify.html
or "fix print"_fix_print.html commands for examples. A '#' or '$' or "fix print"_fix_print.html commands for examples. A '#' or '$'
character that in text between double quotes will not be treated as a character that is in text between double quotes will not be treated as
comment or substituted for as a variable. a comment or substituted for as a variable.
:line :line
@ -380,6 +380,8 @@ of each style or click on the style itself for a full description:
"ave/atom"_fix_ave_atom.html, "ave/atom"_fix_ave_atom.html,
"ave/spatial"_fix_ave_spatial.html, "ave/spatial"_fix_ave_spatial.html,
"ave/time"_fix_ave_time.html, "ave/time"_fix_ave_time.html,
"bond/break"_fix_bond_break.html,
"bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html, "bond/swap"_fix_bond_swap.html,
"com"_fix_com.html, "com"_fix_com.html,
"coord/original"_fix_coord_original.html, "coord/original"_fix_coord_original.html,

4
doc/Section_errors.html
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@ -42,8 +42,8 @@ See the discussion of the <I>loop</I> option in the
</P> </P>
<P>Similarly, the <A HREF = "create_atoms.html">create_atoms</A> command generates a <P>Similarly, the <A HREF = "create_atoms.html">create_atoms</A> command generates a
lattice of atoms. For the same physical system, the ordering and lattice of atoms. For the same physical system, the ordering and
numbering of atoms (atom ID or tag) may be different depending on the numbering of atoms by atom ID may be different depending on the number
number of processors. of processors.
</P> </P>
<P>Some commands use random number generators which may be setup to <P>Some commands use random number generators which may be setup to
produce different random number streams on each processor and hence produce different random number streams on each processor and hence

4
doc/Section_errors.txt
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@ -39,8 +39,8 @@ See the discussion of the {loop} option in the
Similarly, the "create_atoms"_create_atoms.html command generates a Similarly, the "create_atoms"_create_atoms.html command generates a
lattice of atoms. For the same physical system, the ordering and lattice of atoms. For the same physical system, the ordering and
numbering of atoms (atom ID or tag) may be different depending on the numbering of atoms by atom ID may be different depending on the number
number of processors. of processors.
Some commands use random number generators which may be setup to Some commands use random number generators which may be setup to
produce different random number streams on each processor and hence produce different random number streams on each processor and hence

5
doc/angle_hybrid.html
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@ -48,9 +48,8 @@ assigned to other hybrid styles, use the style name (e.g. "harmonic")
appropriate to that style. The BondBond and BondAngle coeffs for that appropriate to that style. The BondBond and BondAngle coeffs for that
angle type will then be ignored. angle type will then be ignored.
</P> </P>
<P>An angle style of <I>none</I> can be specified as an argument to <P>An angle style of <I>none</I> can be specified as the 2nd argument to the
angle_style hybrid and the corresponding angle_coeff commands, if you angle_coeff command, if you desire to turn off certain angle types.
desire to turn off certain angle types.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>

5
doc/angle_hybrid.txt
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@ -45,9 +45,8 @@ assigned to other hybrid styles, use the style name (e.g. "harmonic")
appropriate to that style. The BondBond and BondAngle coeffs for that appropriate to that style. The BondBond and BondAngle coeffs for that
angle type will then be ignored. angle type will then be ignored.
An angle style of {none} can be specified as an argument to An angle style of {none} can be specified as the 2nd argument to the
angle_style hybrid and the corresponding angle_coeff commands, if you angle_coeff command, if you desire to turn off certain angle types.
desire to turn off certain angle types.
[Restrictions:] [Restrictions:]

5
doc/bond_hybrid.html
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@ -41,9 +41,8 @@ coefficients 80.0, 1.2 for K, r0. All other bond types (2-N) would be
computed with a <I>fene</I> potential with coefficients 30.0, 1.5, 1.0, 1.0 computed with a <I>fene</I> potential with coefficients 30.0, 1.5, 1.0, 1.0
for K, R0, epsilon, sigma. for K, R0, epsilon, sigma.
</P> </P>
<P>A bond style of <I>none</I> can be specified as an argument to bond_style <P>A bond style of <I>none</I> can be specified as the 2nd argument to the
hybrid and the corresponding bond_coeff commands, if you desire to bond_coeff command, if you desire to turn off certain bond types.
turn off certain bond types.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>

5
doc/bond_hybrid.txt
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@ -38,9 +38,8 @@ coefficients 80.0, 1.2 for K, r0. All other bond types (2-N) would be
computed with a {fene} potential with coefficients 30.0, 1.5, 1.0, 1.0 computed with a {fene} potential with coefficients 30.0, 1.5, 1.0, 1.0
for K, R0, epsilon, sigma. for K, R0, epsilon, sigma.
A bond style of {none} can be specified as an argument to bond_style A bond style of {none} can be specified as the 2nd argument to the
hybrid and the corresponding bond_coeff commands, if you desire to bond_coeff command, if you desire to turn off certain bond types.
turn off certain bond types.
[Restrictions:] [Restrictions:]

6
doc/dihedral_hybrid.html
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@ -50,9 +50,9 @@ to other hybrid styles, use the style name (e.g. "harmonic")
appropriate to that style. The MiddleBondTorsion, etc coeffs for that appropriate to that style. The MiddleBondTorsion, etc coeffs for that
dihedral type will then be ignored. dihedral type will then be ignored.
</P> </P>
<P>A dihedral style of <I>none</I> can be specified as an argument to <P>A dihedral style of <I>none</I> can be specified as the 2nd argument to the
dihedral_style hybrid and the corresponding dihedral_coeff commands, dihedral_coeff command, if you desire to turn off certain dihedral
if you desire to turn off certain dihedral types. types.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>

6
doc/dihedral_hybrid.txt
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@ -47,9 +47,9 @@ to other hybrid styles, use the style name (e.g. "harmonic")
appropriate to that style. The MiddleBondTorsion, etc coeffs for that appropriate to that style. The MiddleBondTorsion, etc coeffs for that
dihedral type will then be ignored. dihedral type will then be ignored.
A dihedral style of {none} can be specified as an argument to A dihedral style of {none} can be specified as the 2nd argument to the
dihedral_style hybrid and the corresponding dihedral_coeff commands, dihedral_coeff command, if you desire to turn off certain dihedral
if you desire to turn off certain dihedral types. types.
[Restrictions:] [Restrictions:]

12
doc/dump.html
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@ -33,7 +33,7 @@
<I>xtc</I> args = none <I>xtc</I> args = none
<I>xyz</I> args = none <I>xyz</I> args = none
<I>custom</I> args = list of atom attributes <I>custom</I> args = list of atom attributes
possible attributes = tag, mol, type, possible attributes = id, mol, type,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz, vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, q, mux, muy, muz,
@ -41,7 +41,7 @@
angmomx, angmomy, angmomz, angmomx, angmomy, angmomz,
quatw, quati, quatj, quatk, tqx, tqy, tqz, quatw, quati, quatj, quatk, tqx, tqy, tqz,
c_ID, c_ID[N], f_ID, f_ID[N], v_name c_ID, c_ID[N], f_ID, f_ID[N], v_name
tag = atom ID id = atom ID
mol = molecule ID mol = molecule ID
type = atom type type = atom type
x,y,z = unscaled atom coordinates x,y,z = unscaled atom coordinates
@ -69,8 +69,8 @@
</P> </P>
<PRE>dump myDump all atom 100 dump.atom <PRE>dump myDump all atom 100 dump.atom
dump 2 subgroup atom 50 dump.run.bin dump 2 subgroup atom 50 dump.run.bin
dump 4a all custom 100 dump.myforce.* tag type x y vx fx dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce tag type c_myF[3] v_ke dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 1 all xtc 1000 file.xtc dump 1 all xtc 1000 file.xtc
</PRE> </PRE>
<P><B>Description:</B> <P><B>Description:</B>
@ -229,8 +229,8 @@ styles.
<P>This section explains the atom quantities that can be specified as <P>This section explains the atom quantities that can be specified as
part of the <I>custom</I> style. part of the <I>custom</I> style.
</P> </P>
<P>The <I>tag</I>, <I>mol</I>, <I>type</I>, <I>x</I>, <I>y</I>, <I>z</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>, <P>The <I>id</I>, <I>mol</I>, <I>type</I>, <I>x</I>, <I>y</I>, <I>z</I>, <I>vx</I>, <I>vy</I>, <I>vz</I>, <I>fx</I>, <I>fy</I>,
<I>fz</I>, <I>q</I> keywords are self-explanatory. <I>Tag</I> is the atom ID. <I>Mol</I> <I>fz</I>, <I>q</I> keywords are self-explanatory. <I>Id</I> is the atom ID. <I>Mol</I>
is the molecule ID, included in the data file for molecular systems. is the molecule ID, included in the data file for molecular systems.
The <I>x</I>, <I>y</I>, <I>z</I> keywords write atom coordinates "unscaled", in the The <I>x</I>, <I>y</I>, <I>z</I> keywords write atom coordinates "unscaled", in the
appropriate distance <A HREF = "units.html">units</A> (Angstroms, sigma, etc). Use appropriate distance <A HREF = "units.html">units</A> (Angstroms, sigma, etc). Use

12
doc/dump.txt
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@ -24,7 +24,7 @@ args = list of arguments for a particular style :l
{xtc} args = none {xtc} args = none
{xyz} args = none {xyz} args = none
{custom} args = list of atom attributes {custom} args = list of atom attributes
possible attributes = tag, mol, type, possible attributes = id, mol, type,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz, x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz, vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, q, mux, muy, muz,
@ -32,7 +32,7 @@ args = list of arguments for a particular style :l
angmomx, angmomy, angmomz, angmomx, angmomy, angmomz,
quatw, quati, quatj, quatk, tqx, tqy, tqz, quatw, quati, quatj, quatk, tqx, tqy, tqz,
c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name
tag = atom ID id = atom ID
mol = molecule ID mol = molecule ID
type = atom type type = atom type
x,y,z = unscaled atom coordinates x,y,z = unscaled atom coordinates
@ -59,8 +59,8 @@ args = list of arguments for a particular style :l
dump myDump all atom 100 dump.atom dump myDump all atom 100 dump.atom
dump 2 subgroup atom 50 dump.run.bin dump 2 subgroup atom 50 dump.run.bin
dump 4a all custom 100 dump.myforce.* tag type x y vx fx dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce tag type c_myF\[3\] v_ke dump 4b flow custom 100 dump.%.myforce id type c_myF\[3\] v_ke
dump 1 all xtc 1000 file.xtc :pre dump 1 all xtc 1000 file.xtc :pre
[Description:] [Description:]
@ -219,8 +219,8 @@ styles.
This section explains the atom quantities that can be specified as This section explains the atom quantities that can be specified as
part of the {custom} style. part of the {custom} style.
The {tag}, {mol}, {type}, {x}, {y}, {z}, {vx}, {vy}, {vz}, {fx}, {fy}, The {id}, {mol}, {type}, {x}, {y}, {z}, {vx}, {vy}, {vz}, {fx}, {fy},
{fz}, {q} keywords are self-explanatory. {Tag} is the atom ID. {Mol} {fz}, {q} keywords are self-explanatory. {Id} is the atom ID. {Mol}
is the molecule ID, included in the data file for molecular systems. is the molecule ID, included in the data file for molecular systems.
The {x}, {y}, {z} keywords write atom coordinates "unscaled", in the The {x}, {y}, {z} keywords write atom coordinates "unscaled", in the
appropriate distance "units"_units.html (Angstroms, sigma, etc). Use appropriate distance "units"_units.html (Angstroms, sigma, etc). Use

2
doc/fix.html
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@ -108,6 +108,8 @@ list of fix styles available in LAMMPS:
<LI><A HREF = "fix_ave_atom.html">ave/atom</A> - compute per-atom time-averaged quantities <LI><A HREF = "fix_ave_atom.html">ave/atom</A> - compute per-atom time-averaged quantities
<LI><A HREF = "fix_ave_spatial.html">ave/spatial</A> - output per-atom quantities by layer <LI><A HREF = "fix_ave_spatial.html">ave/spatial</A> - output per-atom quantities by layer
<LI><A HREF = "fix_ave_time.html">ave/time</A> - output time-averaged compute quantities <LI><A HREF = "fix_ave_time.html">ave/time</A> - output time-averaged compute quantities
<LI><A HREF = "fix_bond_break.html">bond/break</A> - break bonds on the fly
<LI><A HREF = "fix_bond_create.html">bond/create</A> - create bonds on the fly
<LI><A HREF = "fix_bond_swap.html">bond/swap</A> - Monte Carlo bond swapping <LI><A HREF = "fix_bond_swap.html">bond/swap</A> - Monte Carlo bond swapping
<LI><A HREF = "fix_com.html">com</A> - compute a center-of-mass <LI><A HREF = "fix_com.html">com</A> - compute a center-of-mass
<LI><A HREF = "fix_coord_original.html">coord/original</A> - store original coords of each atom <LI><A HREF = "fix_coord_original.html">coord/original</A> - store original coords of each atom

2
doc/fix.txt
View File

@ -105,6 +105,8 @@ list of fix styles available in LAMMPS:
"ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities "ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
"ave/spatial"_fix_ave_spatial.html - output per-atom quantities by layer "ave/spatial"_fix_ave_spatial.html - output per-atom quantities by layer
"ave/time"_fix_ave_time.html - output time-averaged compute quantities "ave/time"_fix_ave_time.html - output time-averaged compute quantities
"bond/break"_fix_bond_break.html - break bonds on the fly
"bond/create"_fix_bond_create.html - create bonds on the fly
"bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
"com"_fix_com.html - compute a center-of-mass "com"_fix_com.html - compute a center-of-mass
"coord/original"_fix_coord_original.html - store original coords of each atom "coord/original"_fix_coord_original.html - store original coords of each atom

8
doc/fix_wall_reflect.html
View File

@ -43,14 +43,6 @@ the corresponding timestep asymmetrically, energy conservation is only
satisfied to O(dt), rather than to O(dt^2) as it would be for satisfied to O(dt), rather than to O(dt^2) as it would be for
velocity-Verlet integration without reflective walls. velocity-Verlet integration without reflective walls.
</P> </P>
<P>IMPORTANT NOTE: This fix performs its operations at the same point in
the timestep as other time integration fixes, such as <A HREF = "fix_nve.html">fix
nve</A>, <A HREF = "fix_nvt.html">fix nvt</A>, or <A HREF = "fix_npt.html">fix npt</A>.
Thus fix wall/reflect should normally be the last such fix specified
in the input script, since the adjustments it makes to atom
coordinates should come after the changes made by time integration.
LAMMPS will warn you if your fixes are not ordered this way.
</P>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B> <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P> </P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart <P>No information about this fix is written to <A HREF = "restart.html">binary restart

8
doc/fix_wall_reflect.txt
View File

@ -40,14 +40,6 @@ the corresponding timestep asymmetrically, energy conservation is only
satisfied to O(dt), rather than to O(dt^2) as it would be for satisfied to O(dt), rather than to O(dt^2) as it would be for
velocity-Verlet integration without reflective walls. velocity-Verlet integration without reflective walls.
IMPORTANT NOTE: This fix performs its operations at the same point in
the timestep as other time integration fixes, such as "fix
nve"_fix_nve.html, "fix nvt"_fix_nvt.html, or "fix npt"_fix_npt.html.
Thus fix wall/reflect should normally be the last such fix specified
in the input script, since the adjustments it makes to atom
coordinates should come after the changes made by time integration.
LAMMPS will warn you if your fixes are not ordered this way.
[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 No information about this fix is written to "binary restart

6
doc/improper_hybrid.html
View File

@ -49,9 +49,9 @@ to other hybrid styles, use the style name (e.g. "harmonic")
appropriate to that style. The AngleAngle coeffs for that improper appropriate to that style. The AngleAngle coeffs for that improper
type will then be ignored. type will then be ignored.
</P> </P>
<P>An improper style of <I>none</I> can be specified as an argument to <P>An improper style of <I>none</I> can be specified as the 2nd argument to
improper_style hybrid and the corresponding improper_coeff commands, the improper_coeff command, if you desire to turn off certain improper
if you desire to turn off certain improper types. types.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>

6
doc/improper_hybrid.txt
View File

@ -46,9 +46,9 @@ to other hybrid styles, use the style name (e.g. "harmonic")
appropriate to that style. The AngleAngle coeffs for that improper appropriate to that style. The AngleAngle coeffs for that improper
type will then be ignored. type will then be ignored.
An improper style of {none} can be specified as an argument to An improper style of {none} can be specified as the 2nd argument to
improper_style hybrid and the corresponding improper_coeff commands, the improper_coeff command, if you desire to turn off certain improper
if you desire to turn off certain improper types. types.
[Restrictions:] [Restrictions:]

16
doc/pair_gran.html
View File

@ -74,9 +74,19 @@ The tangential force between 2 particles grows according to a
tangential spring and dash-pot model until Ft/Fn = xmu and is then tangential spring and dash-pot model until Ft/Fn = xmu and is then
held at Ft = Fn*xmu until the particles lose contact. held at Ft = Fn*xmu until the particles lose contact.
</P> </P>
<P>For granular styles there are no individual atom type coefficients <P>For granular styles there are no additional coefficients to set for
that can be set via the <A HREF = "pair_coeff.html">pair_coeff</A> command. All each pair of atom types via the <A HREF = "pair_coeff.html">pair_coeff</A> command.
global settings are made via the pair_style command. All settings are global and are made via the pair_style command.
However you must still use the <A HREF = "pair_coeff.html">pair_coeff</A> for all
pairs of granular atom types. For example the command
</P>
<PRE>pair_coeff * *
</PRE>
<P>should be used if all atoms in the simulation interact via a granular
potential. If a granular potential is used as part of <A HREF = "pair_hybrid.html">pair_style
hybrid</A>, then specific atom types can be used in the
pair_coeff command to determine which atoms interact via a granular
potential.
</P> </P>
<P>See the citation below for more discussion of granular potentials. <P>See the citation below for more discussion of granular potentials.
</P> </P>

16
doc/pair_gran.txt
View File

@ -66,9 +66,19 @@ The tangential force between 2 particles grows according to a
tangential spring and dash-pot model until Ft/Fn = xmu and is then tangential spring and dash-pot model until Ft/Fn = xmu and is then
held at Ft = Fn*xmu until the particles lose contact. held at Ft = Fn*xmu until the particles lose contact.
For granular styles there are no individual atom type coefficients For granular styles there are no additional coefficients to set for
that can be set via the "pair_coeff"_pair_coeff.html command. All each pair of atom types via the "pair_coeff"_pair_coeff.html command.
global settings are made via the pair_style command. All settings are global and are made via the pair_style command.
However you must still use the "pair_coeff"_pair_coeff.html for all
pairs of granular atom types. For example the command
pair_coeff * * :pre
should be used if all atoms in the simulation interact via a granular
potential. If a granular potential is used as part of "pair_style
hybrid"_pair_hybrid.html, then specific atom types can be used in the
pair_coeff command to determine which atoms interact via a granular
potential.
See the citation below for more discussion of granular potentials. See the citation below for more discussion of granular potentials.

8
doc/read_data.html
View File

@ -78,6 +78,7 @@ is different than the default.
<LI><I>angle types</I> = # of angle types in system <LI><I>angle types</I> = # of angle types in system
<LI><I>dihedral types</I> = # of dihedral types in system <LI><I>dihedral types</I> = # of dihedral types in system
<LI><I>improper types</I> = # of improper types in system <LI><I>improper types</I> = # of improper types in system
<LI><I>extra bond per atom</I> = leave space for this many new bonds per atom
<LI><I>xlo xhi</I> = simulation box boundaries in x dimension <LI><I>xlo xhi</I> = simulation box boundaries in x dimension
<LI><I>ylo yhi</I> = simulation box boundaries in y dimension <LI><I>ylo yhi</I> = simulation box boundaries in y dimension
<LI><I>zlo zhi</I> = simulation box boundaries in z dimension <LI><I>zlo zhi</I> = simulation box boundaries in z dimension
@ -87,7 +88,7 @@ is different than the default.
In any dimension, the system may be periodic or non-periodic; see the In any dimension, the system may be periodic or non-periodic; see the
<A HREF = "boundary.html">boundary</A> command. <A HREF = "boundary.html">boundary</A> command.
</P> </P>
<P>If the <I>xy xz yz</I> line does not appear, then LAMMPS will set up an <P>If the <I>xy xz yz</I> line does not appear, LAMMPS will set up an
axis-aligned (orthogonal) simulation box. If the line does appear, axis-aligned (orthogonal) simulation box. If the line does appear,
LAMMPS creates a non-orthogonal simulation domain shaped as a LAMMPS creates a non-orthogonal simulation domain shaped as a
parallelepiped with triclinic symmetry. See the <A HREF = "region.html">region parallelepiped with triclinic symmetry. See the <A HREF = "region.html">region
@ -139,6 +140,11 @@ specified box size to layout the 3d grid of processors. A huge
parallel simulation to lose atoms if LAMMPS shrink-wraps the box parallel simulation to lose atoms if LAMMPS shrink-wraps the box
around the atoms. around the atoms.
</P> </P>
<P>The "extra bond per atom" setting should be used if new bonds will be
added to the system when a simulation runs, e.g. by using the <A HREF = "fix_bond_create.html">fix
bond/create</A> command. This will pre-allocate
space in LAMMPS data structures for storing the new bonds.
</P>
<HR> <HR>
<P>These are the section keywords for the body of the file. <P>These are the section keywords for the body of the file.

8
doc/read_data.txt
View File

@ -73,6 +73,7 @@ is different than the default.
{angle types} = # of angle types in system {angle types} = # of angle types in system
{dihedral types} = # of dihedral types in system {dihedral types} = # of dihedral types in system
{improper types} = # of improper types in system {improper types} = # of improper types in system
{extra bond per atom} = leave space for this many new bonds per atom
{xlo xhi} = simulation box boundaries in x dimension {xlo xhi} = simulation box boundaries in x dimension
{ylo yhi} = simulation box boundaries in y dimension {ylo yhi} = simulation box boundaries in y dimension
{zlo zhi} = simulation box boundaries in z dimension {zlo zhi} = simulation box boundaries in z dimension
@ -82,7 +83,7 @@ The initial simulation box size is determined by the lo/hi settings.
In any dimension, the system may be periodic or non-periodic; see the In any dimension, the system may be periodic or non-periodic; see the
"boundary"_boundary.html command. "boundary"_boundary.html command.
If the {xy xz yz} line does not appear, then LAMMPS will set up an If the {xy xz yz} line does not appear, LAMMPS will set up an
axis-aligned (orthogonal) simulation box. If the line does appear, axis-aligned (orthogonal) simulation box. If the line does appear,
LAMMPS creates a non-orthogonal simulation domain shaped as a LAMMPS creates a non-orthogonal simulation domain shaped as a
parallelepiped with triclinic symmetry. See the "region parallelepiped with triclinic symmetry. See the "region
@ -134,6 +135,11 @@ specified box size to layout the 3d grid of processors. A huge
parallel simulation to lose atoms if LAMMPS shrink-wraps the box parallel simulation to lose atoms if LAMMPS shrink-wraps the box
around the atoms. around the atoms.
The "extra bond per atom" setting should be used if new bonds will be
added to the system when a simulation runs, e.g. by using the "fix
bond/create"_fix_bond_create.html command. This will pre-allocate
space in LAMMPS data structures for storing the new bonds.
:line :line
These are the section keywords for the body of the file. These are the section keywords for the body of the file.

17
doc/replicate.html
View File

@ -30,15 +30,14 @@ dimension. A replication factor of 1 in a dimension leaves the
simulation domain unchanged. simulation domain unchanged.
</P> </P>
<P>All properties of the atoms are replicated, including their <P>All properties of the atoms are replicated, including their
velocities, which may or may not be desirable. New atom IDs (tags) velocities, which may or may not be desirable. New atom IDs are
are assigned to new atoms, as are molecule IDs. Bonds and other assigned to new atoms, as are molecule IDs. Bonds and other topology
topology interactions are created between pairs of new atoms as well interactions are created between pairs of new atoms as well as between
as between old and new atoms. This is done by using the image flag old and new atoms. This is done by using the image flag for each atom
for each atom to "unwrap" it out of the periodic box before to "unwrap" it out of the periodic box before replicating it. This
replicating it. This means that molecular bonds you specify in the means that molecular bonds you specify in the original data file that
original data file that span the periodic box should be between two span the periodic box should be between two atoms with image flags
atoms with image flags that differ by 1. This will allow them to be that differ by 1. This will allow them to be unwrapped appropriately.
unwrapped appropriately.
</P> </P>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>
</P> </P>

17
doc/replicate.txt
View File

@ -27,15 +27,14 @@ dimension. A replication factor of 1 in a dimension leaves the
simulation domain unchanged. simulation domain unchanged.
All properties of the atoms are replicated, including their All properties of the atoms are replicated, including their
velocities, which may or may not be desirable. New atom IDs (tags) velocities, which may or may not be desirable. New atom IDs are
are assigned to new atoms, as are molecule IDs. Bonds and other assigned to new atoms, as are molecule IDs. Bonds and other topology
topology interactions are created between pairs of new atoms as well interactions are created between pairs of new atoms as well as between
as between old and new atoms. This is done by using the image flag old and new atoms. This is done by using the image flag for each atom
for each atom to "unwrap" it out of the periodic box before to "unwrap" it out of the periodic box before replicating it. This
replicating it. This means that molecular bonds you specify in the means that molecular bonds you specify in the original data file that
original data file that span the periodic box should be between two span the periodic box should be between two atoms with image flags
atoms with image flags that differ by 1. This will allow them to be that differ by 1. This will allow them to be unwrapped appropriately.
unwrapped appropriately.
[Restrictions:] [Restrictions:]

15
doc/reset_timestep.html
View File

@ -45,6 +45,21 @@ write. See the <A HREF = "undump.html">undump</A> command or <A HREF = "restart
if necessary. New specifications for dump and restart files can be if necessary. New specifications for dump and restart files can be
given after the reset_timestep command is used. given after the reset_timestep command is used.
</P> </P>
<P>This command cannot be used when any fixes are defined that keep track
of time or the timestep in order to perform time-dependent operations.
Examples include the "ave" or "wall" fixes such as <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> or <A HREF = "fix_wall_lj126.html">fix
wall/lj126</A>, and also <A HREF = "fix_indent.html">fix
indent</A>. The wall and indeter fixes allow for a
velocity or other time-dependent parameter to be specified, which
would be messed up by resetting the timestep.
</P>
<P>Restting the timestep will clear the flags for <A HREF = "compute.html">computes</A>
that may have calculated some quantity from a previous run. This
means that quantity cannot be accessed by a variable in between runs
until a new run is performed. See the <A HREF = "variable.html">variable</A>
command for more details.
</P>
<P><B>Related commands:</B> none <P><B>Related commands:</B> none
</P> </P>
<P><B>Default:</B> none <P><B>Default:</B> none

15
doc/reset_timestep.txt
View File

@ -42,6 +42,21 @@ write. See the "undump"_undump.html command or "restart
if necessary. New specifications for dump and restart files can be if necessary. New specifications for dump and restart files can be
given after the reset_timestep command is used. given after the reset_timestep command is used.
This command cannot be used when any fixes are defined that keep track
of time or the timestep in order to perform time-dependent operations.
Examples include the "ave" or "wall" fixes such as "fix
ave/spatial"_fix_ave_spatial.html or "fix
wall/lj126"_fix_wall_lj126.html, and also "fix
indent"_fix_indent.html. The wall and indeter fixes allow for a
velocity or other time-dependent parameter to be specified, which
would be messed up by resetting the timestep.
Restting the timestep will clear the flags for "computes"_compute.html
that may have calculated some quantity from a previous run. This
means that quantity cannot be accessed by a variable in between runs
until a new run is performed. See the "variable"_variable.html
command for more details.
[Related commands:] none [Related commands:] none
[Default:] none [Default:] none

8
doc/run.html
View File

@ -157,6 +157,14 @@ command (e.g. print "Protein Rg = $r" as in the example above). This
means that, if specified, the <I>every</I> option must be the last keyword means that, if specified, the <I>every</I> option must be the last keyword
used. used.
</P> </P>
<P>IMPORTANT NOTE: For the <I>every</I> option, if the command includes a
variable (e.g. $x or ${abc}), and you want the variable to be
evaluated afresh each time the command is invoked, then you should
enclose that command argument in double quotes, as in the "Protein Rg
= $r" example above. If you don't do this, then the variable will be
substituted for only once initially when the run command is parsed,
just as occurs for any other command containing a variable.
</P>
<P>If the <I>pre</I> and <I>post</I> options are set to "no" when used with the <P>If the <I>pre</I> and <I>post</I> options are set to "no" when used with the
<I>every</I> keyword, then the 1st run will do the full setup and the last <I>every</I> keyword, then the 1st run will do the full setup and the last
run will print the full timing summary, but these operations will be run will print the full timing summary, but these operations will be

8
doc/run.txt
View File

@ -150,6 +150,14 @@ command (e.g. print "Protein Rg = $r" as in the example above). This
means that, if specified, the {every} option must be the last keyword means that, if specified, the {every} option must be the last keyword
used. used.
IMPORTANT NOTE: For the {every} option, if the command includes a
variable (e.g. $x or $\{abc\}), and you want the variable to be
evaluated afresh each time the command is invoked, then you should
enclose that command argument in double quotes, as in the "Protein Rg
= $r" example above. If you don't do this, then the variable will be
substituted for only once initially when the run command is parsed,
just as occurs for any other command containing a variable.
If the {pre} and {post} options are set to "no" when used with the If the {pre} and {post} options are set to "no" when used with the
{every} keyword, then the 1st run will do the full setup and the last {every} keyword, then the 1st run will do the full setup and the last
run will print the full timing summary, but these operations will be run will print the full timing summary, but these operations will be

160
doc/special_bonds.html
View File

@ -13,105 +13,125 @@
</H3> </H3>
<P><B>Syntax:</B> <P><B>Syntax:</B>
</P> </P>
<PRE>special_bonds style args <PRE>special_bonds keyword values ...
</PRE> </PRE>
<UL><LI>style = <I>charmm</I> or <I>amber</I> or <I>dihedral</I> or <I>explicit</I> (<I>explicit</I> can be omitted) <UL><LI>one or more keyword/value pairs may be appended
<PRE> <I>charmm</I> args = none <LI>keyword = <I>amber</I> or <I>charmm</I> or <I>fene</I> or <I>lj/coul</I> or <I>lj</I> or <I>coul</I> or <I>dihedral</I> or <I>extra</I>
<I>amber</I> args = none
<I>dihedral</I> args = c1 c2 c3 c4 c5 c6 <PRE> <I>amber</I> values = none
c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified) <I>charmm</I> values = none
c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional) <I>fene</I> values = none
<I>explicit</I> args = c1 c2 c3 c4 c5 c6 <I>lj/coul</I> values = w1,w2,w3
c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified) w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional) <I>lj</I> values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
<I>coul</I> values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
<I>dihedral</I> value = <I>yes</I> or <I>no</I>
<I>extra</I> value = N
N = number of extra 1-2,1-3,1-4 interactions to save space for
</PRE> </PRE>
</UL> </UL>
<P>Examples: <P>Examples:
</P> </P>
<PRE>special_bonds charmm <PRE>special_bonds amber
special_bonds amber special_bonds charmm
special_bonds dihedral 0.0 0.0 0.5 special_bonds fene dihedral no
special_bonds explicit 0 1 1 special_bonds lj/coul 0.0 0.0 0.5 dihedral yes
special_bonds 0 1 1 special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 special_bonds lj/coul 0 1 1 extra 2
</PRE> </PRE>
<P><B>Description:</B> <P><B>Description:</B>
</P> </P>
<P>Set the weighting coefficients for the pairwise force and energy <P>Set weighting coefficients for pairwise energy and force contributions
contributions from atom pairs that are also bonded to each other from atom pairs that are also bonded to each other directly or
directly or indirectly. For Lennard-Jones and Coulombic pairwise indirectly. For Lennard-Jones (LJ) and Coulombic pairwise
interactions, the 1st coefficient is the weighting factor on 1-2 atom interactions, these coefficients come in sets of three. The 1st
pairs, which are those directly bonded to each other. The 2nd coefficient is the weighting factor on 1-2 atom pairs, which are those
coefficient is the weighting factor on 1-3 atom pairs which are those directly bonded to each other. The 2nd coefficient is the weighting
separated by 2 bonds (e.g. the 2 H atoms in a water molecule). The factor on 1-3 atom pairs which are those separated by 2 bonds
3rd coefficient is the weighting factor on 1-4 atom pairs which are (e.g. the two H atoms in a water molecule). The 3rd coefficient is
separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral the weighting factor on 1-4 atom pairs which are those separated by 3
interaction). bonds (e.g. the 1st and 4th atoms in a dihedral interaction). Thus if
the 1-2 coefficient is set to 0.0, then the pairwise interaction is
effectively turned off for all pairs of atoms bonded to each other.
</P> </P>
<P>Note that for purposes of computing weighted pairwise interactions, <P>IMPORTANT NOTE: For purposes of computing weighted pairwise
1-3 and 1-4 interactions are NOT defined from the list of angles or interactions, 1-3 and 1-4 interactions are not defined from the list
dihedrals used by the simulation. Rather, they are inferred of angles or dihedrals used by the simulation. Rather, they are
topologically by the set of bonds defined when atoms are read in from inferred topologically from the set of bonds defined when the
a file (<A HREF = "read_data.html">read_data</A> or simulation is defined from a data or restart file (see
<A HREF = "read_restart.html">read_restart</A>). Thus the set of 1-2,1-3,1-4 <A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
interactions is the same whether angle and dihedral potentials are commands). Thus the set of 1-2,1-3,1-4 interactions that the weights
apply to is the same whether angle and dihedral potentials are
computed or not, and remains the same even if bonds are constrained, computed or not, and remains the same even if bonds are constrained,
or turned off, or removed during a simulation. or turned off, or removed during a simulation.
</P> </P>
<P>The two exceptions to this rule are (a) if the special_bonds <P>The two exceptions to this rule are (a) if the <I>dihedral</I> keyword is
<I>dihedral</I> style is used (see below), or (b) if the set to <I>yes</I> (see below), or (b) if the
<A HREF = "delete_bonds.html">delete_bonds</A> command is used with the <I>special</I> <A HREF = "delete_bonds.html">delete_bonds</A> command is used with the <I>special</I>
option that recomputes the 1-2,1-3,1-4 topologies after bonds are option that recomputes the 1-2,1-3,1-4 topologies after bonds are
deleted; see the <A HREF = "delete_bonds.html">delete_bonds</A> command for more deleted; see the <A HREF = "delete_bonds.html">delete_bonds</A> command for more
details. details.
</P> </P>
<P>The <I>charmm</I> style sets all 3 coefficients to 0.0 for both LJ and <P>The <I>amber</I> keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
Coulombic interactions, which is the default for the CHARMM force interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
field. In pair styles <I>lj/charmm/coul/charmm</I> and is the default for a commonly used version of the AMBER force field,
<I>lj/charmm/coul/long</I> the 1-4 coefficients are defined explicitly, and
these pair-wise contributions are computed in the charmm dihedral
style - see the <A HREF = "pair_coeff.html">pair_coeff</A> and
<A HREF = "dihedral_style.html">dihedral_style</A> commands for more information.
</P>
<P>The <I>amber</I> style sets the 3 coefficients to 0.0 0.0 0.5 for LJ
interactions and to 0.0 0.0 0.8333 for Coulombic interactions, which
is the default for a particular version of the AMBER force field,
where the last value is really 5/6. where the last value is really 5/6.
</P> </P>
<P>The <I>dihedral</I> style requires you to set 3 or 6 coefficients (see the <P>The <I>charmm</I> keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
<I>explicit</I> style), but it turns off the 1-4 weighting factor for LJ and Coulombic interactions, which is the default for a commonly
individual atom pairs if they are not listed as the first and last used version of the CHARMM force field. Note that in pair styles
<I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/long</I> the 1-4 coefficients
are defined explicitly, and these pairwise contributions are computed
as part of the charmm dihedral style - see the
<A HREF = "pair_coeff.html">pair_coeff</A> and <A HREF = "dihedral_style.html">dihedral_style</A>
commands for more information.
</P>
<P>The <I>fene</I> keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
LJ and Coulombic interactions, which is consistent with a
coarse-grained polymer model with <A HREF = "bond_fene.html">FENE bonds</A>.
</P>
<P>The <I>lj/coul</I>, <I>lj</I>, and <I>coul</I> keywords allow the 3 coefficients to
be set explicitly. The <I>lj/coul</I> keyword sets both the LJ and
Coulombic coefficients to the same 3 values. The <I>lj</I> and <I>coul</I>
keywords only set either the LJ or Coulombic coefficients. Use both
of them if you wish to set the LJ coefficients to different values
than the Coulombic coefficients.
</P>
<P>The <I>dihedral</I> keyword allows the 1-4 weighting factor to be ignored
for individual atom pairs if they are not listed as the first and last
atoms in any dihedral defined in the simulation. For example, imagine atoms in any dihedral defined in the simulation. For example, imagine
you have set the 1-4 weighting factor to 0.5 and you have a linear the 1-4 weighting factor is set to 0.5 and you have a linear molecule
molecule with 5 atoms and bonds as follows: 1-2-3-4-5. If your data with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file
file defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
dihedral, then the pairwise interaction between atoms 1 and 4 will be dihedral, then the pairwise interaction between atoms 1 and 4 will
weighted by 0.5, but the interaction between atoms 2 and 5 will be always be weighted by 0.5, but different force fields use different
unaffected (full weighting of 1.0). Note that if any of the other rules for weighting the pairwise interaction between atoms 2 and 5.
special_bond styles are used, then the 2,5 interaction would also be If the <I>dihedral</I> keyword is specified as <I>yes</I>, then the pairwise
weighted by 0.5. The <I>dihedral</I> style is provided because some force interaction between atoms 2 and 5 will be unaffected (full weighting
fields follow this rule. of 1.0). If the <I>dihedral</I> keyword is specified as <I>no</I> which is the
default, then the 2,5 interaction will also be weighted by 0.5.
</P> </P>
<P>The <I>explicit</I> style requires you to set 3 or 6 coefficients directly. <P>The <I>extra</I> keyword is used when additional bonds will be created
If 3 are specified, they are used for both LJ and Coulombic during a simulation run, e.g. by the <A HREF = "fix_bond_create.html">fix
interactions. If 6 are specified then the first 3 are LJ coefficients bond/create</A> command. A list of 1-2,1-3,1-4
and the second 3 are Coulombic coefficients. Note that the <I>explicit</I> neighbors for each atom is calculated and stored by LAMMPS. If new
keyword itself is optional; the special_bonds command can just take 3 bonds are created, the list needs to grow. Using the <I>extra</I> keyword
or 6 numeric arguments by themselves. leaves empty space in the list for N additional bonds to be added. If
</P> you do not do this, you may get an error when bonds are added.
<P>IMPORTANT NOTE: For a <A HREF = "units.html">lj units</A> system with <A HREF = "bond_fene.html">FENE
bonds</A> a setting of special bonds 0 1 1 should be used.
</P> </P>
<P><B>Restrictions:</B> none <P><B>Restrictions:</B> none
</P> </P>
<P><B>Related commands:</B> <P><B>Related commands:</B>
</P> </P>
<P><A HREF = "delete_bonds.html">delete_bonds</A> <P><A HREF = "delete_bonds.html">delete_bonds</A>, <A HREF = "fix_bond_create.html">fix bond/create</A>
</P> </P>
<P><B>Default:</B> <P><B>Default:</B>
</P> </P>
<PRE>special_bonds 0.0 0.0 0.0 <P>All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
</PRE> dihedral = no, and extra = 0.
</P>
</HTML> </HTML>

155
doc/special_bonds.txt
View File

@ -10,101 +10,120 @@ special_bonds command :h3
[Syntax:] [Syntax:]
special_bonds style args :pre special_bonds keyword values ... :pre
style = {charmm} or {amber} or {dihedral} or {explicit} ({explicit} can be omitted) :ulb,l one or more keyword/value pairs may be appended :ulb,l
{charmm} args = none keyword = {amber} or {charmm} or {fene} or {lj/coul} or {lj} or {coul} or {dihedral} or {extra} :l
{amber} args = none {amber} values = none
{dihedral} args = c1 c2 c3 c4 c5 c6 {charmm} values = none
c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified) {fene} values = none
c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional) {lj/coul} values = w1,w2,w3
{explicit} args = c1 c2 c3 c4 c5 c6 w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
c1,c2,c3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions (and Coulomb if c4,c5,c6 are not specified) {lj} values = w1,w2,w3
c4,c5,c6 = weights (0.0 to 1.0) on pairwise Coulomb interactions (optional) :pre w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
{coul} values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
{dihedral} value = {yes} or {no}
{extra} value = N
N = number of extra 1-2,1-3,1-4 interactions to save space for :pre
:ule :ule
Examples: Examples:
special_bonds charmm
special_bonds amber special_bonds amber
special_bonds dihedral 0.0 0.0 0.5 special_bonds charmm
special_bonds explicit 0 1 1 special_bonds fene dihedral no
special_bonds 0 1 1 special_bonds lj/coul 0.0 0.0 0.5 dihedral yes
special_bonds 0.0 0.0 1.0 0.0 0.0 0.5 :pre special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
special_bonds lj/coul 0 1 1 extra 2 :pre
[Description:] [Description:]
Set the weighting coefficients for the pairwise force and energy Set weighting coefficients for pairwise energy and force contributions
contributions from atom pairs that are also bonded to each other from atom pairs that are also bonded to each other directly or
directly or indirectly. For Lennard-Jones and Coulombic pairwise indirectly. For Lennard-Jones (LJ) and Coulombic pairwise
interactions, the 1st coefficient is the weighting factor on 1-2 atom interactions, these coefficients come in sets of three. The 1st
pairs, which are those directly bonded to each other. The 2nd coefficient is the weighting factor on 1-2 atom pairs, which are those
coefficient is the weighting factor on 1-3 atom pairs which are those directly bonded to each other. The 2nd coefficient is the weighting
separated by 2 bonds (e.g. the 2 H atoms in a water molecule). The factor on 1-3 atom pairs which are those separated by 2 bonds
3rd coefficient is the weighting factor on 1-4 atom pairs which are (e.g. the two H atoms in a water molecule). The 3rd coefficient is
separated by 3 bonds (e.g. the 1st and 4th atoms in a dihedral the weighting factor on 1-4 atom pairs which are those separated by 3
interaction). bonds (e.g. the 1st and 4th atoms in a dihedral interaction). Thus if
the 1-2 coefficient is set to 0.0, then the pairwise interaction is
effectively turned off for all pairs of atoms bonded to each other.
Note that for purposes of computing weighted pairwise interactions, IMPORTANT NOTE: For purposes of computing weighted pairwise
1-3 and 1-4 interactions are NOT defined from the list of angles or interactions, 1-3 and 1-4 interactions are not defined from the list
dihedrals used by the simulation. Rather, they are inferred of angles or dihedrals used by the simulation. Rather, they are
topologically by the set of bonds defined when atoms are read in from inferred topologically from the set of bonds defined when the
a file ("read_data"_read_data.html or simulation is defined from a data or restart file (see
"read_restart"_read_restart.html). Thus the set of 1-2,1-3,1-4 "read_data"_read_data.html or "read_restart"_read_restart.html
interactions is the same whether angle and dihedral potentials are commands). Thus the set of 1-2,1-3,1-4 interactions that the weights
apply to is the same whether angle and dihedral potentials are
computed or not, and remains the same even if bonds are constrained, computed or not, and remains the same even if bonds are constrained,
or turned off, or removed during a simulation. or turned off, or removed during a simulation.
The two exceptions to this rule are (a) if the special_bonds The two exceptions to this rule are (a) if the {dihedral} keyword is
{dihedral} style is used (see below), or (b) if the set to {yes} (see below), or (b) if the
"delete_bonds"_delete_bonds.html command is used with the {special} "delete_bonds"_delete_bonds.html command is used with the {special}
option that recomputes the 1-2,1-3,1-4 topologies after bonds are option that recomputes the 1-2,1-3,1-4 topologies after bonds are
deleted; see the "delete_bonds"_delete_bonds.html command for more deleted; see the "delete_bonds"_delete_bonds.html command for more
details. details.
The {charmm} style sets all 3 coefficients to 0.0 for both LJ and The {amber} keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
Coulombic interactions, which is the default for the CHARMM force interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
field. In pair styles {lj/charmm/coul/charmm} and is the default for a commonly used version of the AMBER force field,
{lj/charmm/coul/long} the 1-4 coefficients are defined explicitly, and
these pair-wise contributions are computed in the charmm dihedral
style - see the "pair_coeff"_pair_coeff.html and
"dihedral_style"_dihedral_style.html commands for more information.
The {amber} style sets the 3 coefficients to 0.0 0.0 0.5 for LJ
interactions and to 0.0 0.0 0.8333 for Coulombic interactions, which
is the default for a particular version of the AMBER force field,
where the last value is really 5/6. where the last value is really 5/6.
The {dihedral} style requires you to set 3 or 6 coefficients (see the The {charmm} keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
{explicit} style), but it turns off the 1-4 weighting factor for LJ and Coulombic interactions, which is the default for a commonly
individual atom pairs if they are not listed as the first and last used version of the CHARMM force field. Note that in pair styles
{lj/charmm/coul/charmm} and {lj/charmm/coul/long} the 1-4 coefficients
are defined explicitly, and these pairwise contributions are computed
as part of the charmm dihedral style - see the
"pair_coeff"_pair_coeff.html and "dihedral_style"_dihedral_style.html
commands for more information.
The {fene} keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
LJ and Coulombic interactions, which is consistent with a
coarse-grained polymer model with "FENE bonds"_bond_fene.html.
The {lj/coul}, {lj}, and {coul} keywords allow the 3 coefficients to
be set explicitly. The {lj/coul} keyword sets both the LJ and
Coulombic coefficients to the same 3 values. The {lj} and {coul}
keywords only set either the LJ or Coulombic coefficients. Use both
of them if you wish to set the LJ coefficients to different values
than the Coulombic coefficients.
The {dihedral} keyword allows the 1-4 weighting factor to be ignored
for individual atom pairs if they are not listed as the first and last
atoms in any dihedral defined in the simulation. For example, imagine atoms in any dihedral defined in the simulation. For example, imagine
you have set the 1-4 weighting factor to 0.5 and you have a linear the 1-4 weighting factor is set to 0.5 and you have a linear molecule
molecule with 5 atoms and bonds as follows: 1-2-3-4-5. If your data with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file
file defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
dihedral, then the pairwise interaction between atoms 1 and 4 will be dihedral, then the pairwise interaction between atoms 1 and 4 will
weighted by 0.5, but the interaction between atoms 2 and 5 will be always be weighted by 0.5, but different force fields use different
unaffected (full weighting of 1.0). Note that if any of the other rules for weighting the pairwise interaction between atoms 2 and 5.
special_bond styles are used, then the 2,5 interaction would also be If the {dihedral} keyword is specified as {yes}, then the pairwise
weighted by 0.5. The {dihedral} style is provided because some force interaction between atoms 2 and 5 will be unaffected (full weighting
fields follow this rule. of 1.0). If the {dihedral} keyword is specified as {no} which is the
default, then the 2,5 interaction will also be weighted by 0.5.
The {explicit} style requires you to set 3 or 6 coefficients directly. The {extra} keyword is used when additional bonds will be created
If 3 are specified, they are used for both LJ and Coulombic during a simulation run, e.g. by the "fix
interactions. If 6 are specified then the first 3 are LJ coefficients bond/create"_fix_bond_create.html command. A list of 1-2,1-3,1-4
and the second 3 are Coulombic coefficients. Note that the {explicit} neighbors for each atom is calculated and stored by LAMMPS. If new
keyword itself is optional; the special_bonds command can just take 3 bonds are created, the list needs to grow. Using the {extra} keyword
or 6 numeric arguments by themselves. leaves empty space in the list for N additional bonds to be added. If
you do not do this, you may get an error when bonds are added.
IMPORTANT NOTE: For a "lj units"_units.html system with "FENE
bonds"_bond_fene.html a setting of special bonds 0 1 1 should be used.
[Restrictions:] none [Restrictions:] none
[Related commands:] [Related commands:]
"delete_bonds"_delete_bonds.html "delete_bonds"_delete_bonds.html, "fix bond/create"_fix_bond_create.html
[Default:] [Default:]
special_bonds 0.0 0.0 0.0 :pre All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
dihedral = no, and extra = 0.

264
doc/variable.html
View File

@ -69,17 +69,18 @@ evaluation later in the input script or during a simulation.
referenced elsewhere in an input script to become part of a new input referenced elsewhere in an input script to become part of a new input
command. For variable styles that store multiple strings, the command. For variable styles that store multiple strings, the
<A HREF = "next.html">next</A> command can be used to increment which string is <A HREF = "next.html">next</A> command can be used to increment which string is
assigned to the variable. Variables of style <I>equal</I> can be evaluated assigned to the variable. Variables of style <I>equal</I> store a formula
to produce a single numeric value which can be output either directly which when evaluated produces a single numeric value which can be
(see the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix print</A>, and <A HREF = "run.html">run output either directly (see the <A HREF = "print.html">print</A>, <A HREF = "fix_print.html">fix
every</A> commands) or as part of thermodynamic output (see the print</A>, and <A HREF = "run.html">run every</A> commands) or as part
<A HREF = "thermo_style.html">thermo_style</A> command), or used as input to an of thermodynamic output (see the <A HREF = "thermo_style.html">thermo_style</A>
averaging fix (see the <A HREF = "fix_ave/time">fix ave/time</A> command). command), or used as input to an averaging fix (see the <A HREF = "fix_ave/time">fix
Variables of style <I>atom</I> can be evaluated to produce one numeric ave/time</A> command). Variables of style <I>atom</I> store a
value per atom which can be output to a dump file (see the <A HREF = "dump.html">dump formula which when evaluated produces one numeric value per atom which
custom</A> command) or used as input to an averaging fix (see can be output to a dump file (see the <A HREF = "dump.html">dump custom</A> command)
the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> and <A HREF = "fix_ave_atom.html">fix or used as input to an averaging fix (see the <A HREF = "fix_ave_spatial.html">fix
ave/atom</A> commands). ave/spatial</A> and <A HREF = "fix_ave_atom.html">fix ave/atom</A>
commands).
</P> </P>
<P>In the discussion that follows, the "name" of the variable is the <P>In the discussion that follows, the "name" of the variable is the
arbitrary string that is the 1st argument in the variable command. arbitrary string that is the 1st argument in the variable command.
@ -92,6 +93,12 @@ evaluation of the string. Note that the same string can generate
different values when it is evaluated at different times during a different values when it is evaluated at different times during a
simulation. simulation.
</P> </P>
<P>IMPORTANT NOTE: When the input script line that defines a variable of
style <I>equal</I> or <I>atom</I> that contain a formula is encountered, the
formula is NOT immediately evaluated and the result stored. See the
discussion below about "Immediate Evaluation of Variables" if you want
to do this.
</P>
<P>IMPORTANT NOTE: When a variable command is encountered in the input <P>IMPORTANT NOTE: When a variable command is encountered in the input
script and the variable name has already been specified, the command script and the variable name has already been specified, the command
is ignored. This means variables can NOT be re-defined in an input is ignored. This means variables can NOT be re-defined in an input
@ -104,9 +111,9 @@ script.
</P> </P>
<P>There are two exceptions to this rule. First, variables of style <P>There are two exceptions to this rule. First, variables of style
<I>equal</I> and <I>atom</I> ARE redefined each time the command is encountered. <I>equal</I> and <I>atom</I> ARE redefined each time the command is encountered.
This allows them to be reset, when their formulas contain a This only changes their associated formula if the formula contains a
substitution for another variable, e.g. $x. This can be useful in a substitution for another variable, e.g. $x. But that can be useful,
loop. for example, in a loop.
</P> </P>
<P>Second, as described below, if a variable is iterated on to the end of <P>Second, as described below, if a variable is iterated on to the end of
its list of strings via the <A HREF = "next.html">next</A> command, it is removed its list of strings via the <A HREF = "next.html">next</A> command, it is removed
@ -214,7 +221,10 @@ atom whenever it is evaluated.
different stages of the input script or at different times during a different stages of the input script or at different times during a
run. For example, if an <I>equal</I> variable is used in a <A HREF = "fix_print.html">fix run. For example, if an <I>equal</I> variable is used in a <A HREF = "fix_print.html">fix
print</A> command, different values could be printed each print</A> command, different values could be printed each
timestep it was invoked. timestep it was invoked. If you want a variable to be evaluated
immediately, so that the result is stored by the variable instead of
the string, see the section below on "Immediate Evaluation of
Variables".
</P> </P>
<P>The next command cannot be used with <I>equal</I> or <I>atom</I> style <P>The next command cannot be used with <I>equal</I> or <I>atom</I> style
variables, since there is only one string. variables, since there is only one string.
@ -253,10 +263,17 @@ can use formula elements that produce either global values or per-atom
values. values.
</P> </P>
<P>The thermo keywords allowed in a formula are those defined by the <P>The thermo keywords allowed in a formula are those defined by the
"thermo_style custom" command. Since many thermodynamic quantities "thermo_style custom" command. Thermo keywords that require a
are only computable after the a simulation has begun, these keywords <A HREF = "compute.html">compute</A> to calculate their values such as "temp" or
cannot be used if a variable is evaluated before the first simulation "press", use computes stored and invoked by the thermo_style command.
begins. This means that you can only use those keywords in a variable if the
style you are using with the thermo_style command (and the thermo
keywords associated with that style) also define and use the needed
compute. Note that some thermo keywords use a compute indirectly to
calculate their value (e.g. the enthalpy keyword uses temp, pe, and
pressure). If a variable is evaluated in an input script (not during
a run), then the values accessed by the thermo keyword must be
current. See the discussion below about "Variable Accuracy".
</P> </P>
<P>Math operations are written in the usual way, where the "x" and "y" in <P>Math operations are written in the usual way, where the "x" and "y" in
the examples above can be another section of the formula. Operators the examples above can be another section of the formula. Operators
@ -300,7 +317,10 @@ See the doc pages for individual computes to see which ones calculate
global versus per-atom quantities. If the compute reference contains global versus per-atom quantities. If the compute reference contains
empty brackets, then per-atom values calculated by the compute are empty brackets, then per-atom values calculated by the compute are
accessed. Otherwise a single value (global or per-atom) calculated by accessed. Otherwise a single value (global or per-atom) calculated by
the compute is accessed. the compute is accessed. If a variable containing a compute is
evaluated in an input script (not during a run), then the values
accessed by the compute must be current. See the discussion below
about "Variable Accuracy".
</P> </P>
<P>The different kinds of compute references are as follows. M is a <P>The different kinds of compute references are as follows. M is a
positive integer <= the number of vector values calculated by the positive integer <= the number of vector values calculated by the
@ -321,14 +341,17 @@ actual ID of the fix defined elsewhere in the input script. See the
doc pages for individual computes to see which ones calculate global doc pages for individual computes to see which ones calculate global
versus per-atom quantities. If the fix reference contains empty versus per-atom quantities. If the fix reference contains empty
brackets, then per-atom values calculated by the fix are accessed. brackets, then per-atom values calculated by the fix are accessed.
Otherwise a single value (global or per-atom) calculated by the Otherwise a single value (global or per-atom) calculated by the fix is
fix is accessed. accessed.
</P> </P>
<P>Note that some fixes only generate quantities on certain timesteps. <P>Note that some fixes only generate quantities on certain timesteps.
If a variable attempts to access the fix on non-allowed timesteps, an If a variable attempts to access the fix on non-allowed timesteps, an
error is generated. For example, the <A HREF = "fix_ave_time.html">fix ave/time</A> error is generated. For example, the <A HREF = "fix_ave_time.html">fix ave/time</A>
command may only generate averaged quantities every 100 steps. See command may only generate averaged quantities every 100 steps. See
the doc pages for individual fix commands for details. the doc pages for individual fix commands for details. If a variable
containing a fix is evaluated in an input script (not during a run),
then the values accessed by the fix should be current. See the
discussion below about "Variable Accuracy".
</P> </P>
<P>The different kinds of fix references are exactly the same as the <P>The different kinds of fix references are exactly the same as the
compute references listed in the above table, where "c_" is replaced compute references listed in the above table, where "c_" is replaced
@ -358,48 +381,177 @@ print $a
</P> </P>
<HR> <HR>
<P>It is useful to understand the distinction between referencing a <P>Immediate Evaluation of Variables:
variable in a formula using the $x form instead of v_x. There is a
subtle difference between the two references that has to do with when
the evaluation of the included variable is done.
</P> </P>
<P>Referencing the variable as $x, the value of the include variable is <P>There is a difference between referencing a variable with a leading $
substituted for immediately when the line is read from the input sign (e.g. $x or ${abc}) versus with a leading "v_" (e.g. v_x or
script, just as it would be in other input script command. v_abc). The former can be used in any command, including a variable
command, to force the immediate evaluation of the referenced variable
and the substitution of its value into the command. The latter is a
required kind of argument to some commands (e.g. the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A> or <A HREF = "dump.html">dump custom</A> or
<A HREF = "thermo_style.html">thermo_style</A> commands) if you wish it to evaluate
a variable periodically during a run. It can also be used in a
variable formula if you wish to reference a second variable. The
second variable will be evaluated whenever the first variable is
evaluated.
</P> </P>
<P>This could be the desired behavior if a static value is desired. Or <P>As an example, suppose you use this command in your input script to
it could be the desired behavior for an equal-style variable if the define the variable "v" as
variable command appears in a loop (see the <A HREF = "jump.html">jump</A> and
<A HREF = "next.html">next</A> commands), since the substitution will be performed
anew each time thru the loop as the command is re-read. Note that if
the variable formula is enclosed in double quotes, this prevents
variable substitution and thus an error will be generated when the
variable formula is evaluated.
</P> </P>
<P>Referencing the variable as v_x, the value of the included variable <PRE>variable v equal vol
will not be accessed until the variable formula is evaluated. Thus
the value may change each time the evaluation is performed. This may
also be desired behavior.
</P>
<P>As an example, if the current simulation box volume is 1000.0, then
these lines:
</P>
<PRE>variable x equal vol
variable y equal 2*$x
</PRE> </PRE>
<P>will associate the equation string "2*1000.0" with variable y. <P>before a run where the simulation box size changes. You might think
this will assign the initial volume to the variable "v". That is not
the case. Rather it assigns a formula which evaluates the volume
(using the thermo_style keyword "vol") to the variable "v". If you
use the variable "v" in some other command like "fix ave/time" then
the current volume of the box will be evaluated continuously during
the run.
</P> </P>
<P>By contrast, these lines: <P>If you want to store the initial volume of the system, you can do it
this way:
</P> </P>
<PRE>variable x equal vol <PRE>variable v equal vol
variable y equal 2*v_x variable v0 equal $v
</PRE> </PRE>
<P>will associate the equation string "2*v_x" with variable y. <P>The second command will force "v" to be evaluated (yielding the
initial volume) and assign that value to the variable "v0". Thus the
command
</P> </P>
<P>Thus if the variable y were evaluated periodically during a run where <PRE>thermo_style custom step v_v v_v0
the box volume changed, the resulting value would always be 2000.0 for </PRE>
the first case, but would change dynamically for the second case. <P>would print out both the current and initial volume periodically
during the run.
</P> </P>
<P>Note that it is a mistake to enclose a variable formula in double
quotes if it contains variables preceeded by $ signs. For example,
</P>
<PRE>variable vratio equal "${vfinal}/${v0}"
</PRE>
<P>This is because the quotes prevent variable substitution (see <A HREF = "Section_commands.html#3_2">this
section</A> on parsing input script commands),
and thus an error will occur when the formula for "vratio" is
evaluated later.
</P>
<HR>
<P>Variable Accuracy:
</P>
<P>Obviously, LAMMPS attempts to evaluate variables containing formulas
(<I>equal</I> and <I>atom</I> style variables) accurately whenever the
evaluation is performed. Depending on what is included in the
formula, this may require invoking a <A HREF = "compute.html">compute</A>, either
directly or indirectly via a thermo keyword, or accessing a value
calculated and stored by a <A HREF = "fix.html">fix</A>. If the compute is one that
calculates the pressure or energy of the system, then these quantities
need to be tallied during the evaluation of the interatomic potentials
(pair, bond, etc) on timesteps that the variable will need the values.
</P>
<P>LAMMPS keeps track of all of this during a <A HREF = "run.html">run</A> or <A HREF = "minimize.html">energy
minimization</A>. An error will be generated if you
attempt to evaluate a variable on timesteps when it cannot produce
accurate values. For example, if a <A HREF = "thermo_style.html">thermo_style
custom</A> command prints a variable which accesses
values stored by a <A HREF = "fix_ave_time.html">fix ave/time</A> command and the
timesteps on which thermo output is generated are not multiples of the
averaging frequency used in the fix command, then it is an error.
</P>
<P>However, your input script can also require variables to be evaluated
before or after or inbetween runs. In this case, one of three things
may happen.
</P>
<P>(1) The variable may be evaluated accurately. If it contains
references to a compute or fix, and these values were calculated and
stored on the last timestep of a preceeding run, then they can be
accessed and used by the variable.
</P>
<P>(2) LAMMPS may not be able to evaluate the variable and generate an
error. For example, if the variable formula requires a
<A HREF = "compute.html">compute</A> to be invoked, either directly or indirectly
via a thermo keyword, then the variable cannot be evaluated before the
first run has occurred. The general rule is that if a variable uses a
value calculated by a compute, and the variable is not being evaluated
during a run, then the variable will not invoke the compute. Instead,
it can only use the value stored by the compute, which for accuracy
requires that the compute was already invoked on the same timestep
during a preceeding run.
</P>
<P>Thus the way to get around this error is to perform a 0-timestep run
before using the variable. For example, these commands
</P>
<PRE>variable t equal temp
print "Initial temperature = $t"
run 1000
</PRE>
<P>will generate an error if the run is the first run specified in the
input script, because generating a value for the "t" variable requires
a compute for calculating the temperature to be invoked.
</P>
<P>However, this sequence of commands would be fine:
</P>
<PRE>run 0
variable t equal temp
print "Initial temperature = $t"
run 1000
</PRE>
<P>The 0-timestep run initializes and invokes various computes, including
the one for temperature, so that the value it stores is current and
can be accessed by the variable "t" after the run has completed. Note
that a 0-timestep run does not alter the state of the system, so it
does not change the input state for the 1000-timestep run that
follows. Also note, that the 0-timestep run must actually use and
invoke the compute in question (e.g. via <A HREF = "thermo_style.html">thermo</A> or
<A HREF = "dump.html">dump</A> output) in order for it to enable the compute to be
used in a variable after the run.
</P>
<P>Note that unlike computes, <A HREF = "fix.html">fixes</A> will never generate an
error if their values are accessed by a variable in between runs.
They always return some value to the variable. However, this value
may not be what you expect if the fix has not yet calculated the
quantity of interest. For example, the <A HREF = "fix_indent.html">fix indent</A>
command stores the force on the indenter. But this is not computed
until a run is performed. Thus if a variable attempts to print this
value before the first run, values of zero will be output. Again,
performing a 0-timestep run before printing the variable has the
desired effect.
</P>
<P>(3) The variable may be evaluated incorrectly. And LAMMPS may have
no way to detect this has occurred. Consider the following sequence
of commands:
</P>
<PRE>pair_coeff 1 1 1.0 1.0
run 1000
pair_coeff 1 1 1.5 1.0
variable e equal pe
print "Final potential energy = $e"
</PRE>
<P>The first run is performed using one setting for the pairwise
potential defined by the <A HREF = "pair_style.html">pair_style</A> and
<A HREF = "pair_coeff.html">pair_coeff</A> commands. The potential energy is
evaluated on the final timestep and stored by the <A HREF = "compute_pe.html">compute
pe</A> compute (this is done by the
<A HREF = "thermo_style.html">thermo_style</A> command). Then a pair coefficient is
changed, altering the potential energy of the system. When the
potential energy is printed via the "e" variable, LAMMPS will use the
potential energy value stored by the <A HREF = "compute_pe.html">compute pe</A>
compute, thinking it is current. There are many other commands which
could alter the state of the system between runs, causing a variable
to evaluate incorrectly.
</P>
<P>The solution to this issue is the same as for case (2) above, namely
to perform a 0-timestep run before the variable is evaluated to insure
the system is up-to-date. For example, this sequence of commands
would print a potential energy that reflected the changed pairwise
coefficient:
</P>
<PRE>pair_coeff 1 1 1.0 1.0
run 1000
pair_coeff 1 1 1.5 1.0
run 0
variable e equal pe
print "Final potential energy = $e"
</PRE>
<HR> <HR>
<P><B>Restrictions:</B> <P><B>Restrictions:</B>

260
doc/variable.txt
View File

@ -63,17 +63,18 @@ Variables can be used in several ways in LAMMPS. A variable can be
referenced elsewhere in an input script to become part of a new input referenced elsewhere in an input script to become part of a new input
command. For variable styles that store multiple strings, the command. For variable styles that store multiple strings, the
"next"_next.html command can be used to increment which string is "next"_next.html command can be used to increment which string is
assigned to the variable. Variables of style {equal} can be evaluated assigned to the variable. Variables of style {equal} store a formula
to produce a single numeric value which can be output either directly which when evaluated produces a single numeric value which can be
(see the "print"_print.html, "fix print"_fix_print.html, and "run output either directly (see the "print"_print.html, "fix
every"_run.html commands) or as part of thermodynamic output (see the print"_fix_print.html, and "run every"_run.html commands) or as part
"thermo_style"_thermo_style.html command), or used as input to an of thermodynamic output (see the "thermo_style"_thermo_style.html
averaging fix (see the "fix ave/time"_fix_ave/time command). command), or used as input to an averaging fix (see the "fix
Variables of style {atom} can be evaluated to produce one numeric ave/time"_fix_ave/time command). Variables of style {atom} store a
value per atom which can be output to a dump file (see the "dump formula which when evaluated produces one numeric value per atom which
custom"_dump.html command) or used as input to an averaging fix (see can be output to a dump file (see the "dump custom"_dump.html command)
the "fix ave/spatial"_fix_ave_spatial.html and "fix or used as input to an averaging fix (see the "fix
ave/atom"_fix_ave_atom.html commands). ave/spatial"_fix_ave_spatial.html and "fix ave/atom"_fix_ave_atom.html
commands).
In the discussion that follows, the "name" of the variable is the In the discussion that follows, the "name" of the variable is the
arbitrary string that is the 1st argument in the variable command. arbitrary string that is the 1st argument in the variable command.
@ -86,6 +87,12 @@ evaluation of the string. Note that the same string can generate
different values when it is evaluated at different times during a different values when it is evaluated at different times during a
simulation. simulation.
IMPORTANT NOTE: When the input script line that defines a variable of
style {equal} or {atom} that contain a formula is encountered, the
formula is NOT immediately evaluated and the result stored. See the
discussion below about "Immediate Evaluation of Variables" if you want
to do this.
IMPORTANT NOTE: When a variable command is encountered in the input IMPORTANT NOTE: When a variable command is encountered in the input
script and the variable name has already been specified, the command script and the variable name has already been specified, the command
is ignored. This means variables can NOT be re-defined in an input is ignored. This means variables can NOT be re-defined in an input
@ -98,9 +105,9 @@ script.
There are two exceptions to this rule. First, variables of style There are two exceptions to this rule. First, variables of style
{equal} and {atom} ARE redefined each time the command is encountered. {equal} and {atom} ARE redefined each time the command is encountered.
This allows them to be reset, when their formulas contain a This only changes their associated formula if the formula contains a
substitution for another variable, e.g. $x. This can be useful in a substitution for another variable, e.g. $x. But that can be useful,
loop. for example, in a loop.
Second, as described below, if a variable is iterated on to the end of Second, as described below, if a variable is iterated on to the end of
its list of strings via the "next"_next.html command, it is removed its list of strings via the "next"_next.html command, it is removed
@ -208,7 +215,10 @@ Note that {equal} and {atom} variables can produce different values at
different stages of the input script or at different times during a different stages of the input script or at different times during a
run. For example, if an {equal} variable is used in a "fix run. For example, if an {equal} variable is used in a "fix
print"_fix_print.html command, different values could be printed each print"_fix_print.html command, different values could be printed each
timestep it was invoked. timestep it was invoked. If you want a variable to be evaluated
immediately, so that the result is stored by the variable instead of
the string, see the section below on "Immediate Evaluation of
Variables".
The next command cannot be used with {equal} or {atom} style The next command cannot be used with {equal} or {atom} style
variables, since there is only one string. variables, since there is only one string.
@ -248,10 +258,17 @@ can use formula elements that produce either global values or per-atom
values. values.
The thermo keywords allowed in a formula are those defined by the The thermo keywords allowed in a formula are those defined by the
"thermo_style custom" command. Since many thermodynamic quantities "thermo_style custom" command. Thermo keywords that require a
are only computable after the a simulation has begun, these keywords "compute"_compute.html to calculate their values such as "temp" or
cannot be used if a variable is evaluated before the first simulation "press", use computes stored and invoked by the thermo_style command.
begins. This means that you can only use those keywords in a variable if the
style you are using with the thermo_style command (and the thermo
keywords associated with that style) also define and use the needed
compute. Note that some thermo keywords use a compute indirectly to
calculate their value (e.g. the enthalpy keyword uses temp, pe, and
pressure). If a variable is evaluated in an input script (not during
a run), then the values accessed by the thermo keyword must be
current. See the discussion below about "Variable Accuracy".
Math operations are written in the usual way, where the "x" and "y" in Math operations are written in the usual way, where the "x" and "y" in
the examples above can be another section of the formula. Operators the examples above can be another section of the formula. Operators
@ -295,7 +312,10 @@ See the doc pages for individual computes to see which ones calculate
global versus per-atom quantities. If the compute reference contains global versus per-atom quantities. If the compute reference contains
empty brackets, then per-atom values calculated by the compute are empty brackets, then per-atom values calculated by the compute are
accessed. Otherwise a single value (global or per-atom) calculated by accessed. Otherwise a single value (global or per-atom) calculated by
the compute is accessed. the compute is accessed. If a variable containing a compute is
evaluated in an input script (not during a run), then the values
accessed by the compute must be current. See the discussion below
about "Variable Accuracy".
The different kinds of compute references are as follows. M is a The different kinds of compute references are as follows. M is a
positive integer <= the number of vector values calculated by the positive integer <= the number of vector values calculated by the
@ -314,14 +334,17 @@ actual ID of the fix defined elsewhere in the input script. See the
doc pages for individual computes to see which ones calculate global doc pages for individual computes to see which ones calculate global
versus per-atom quantities. If the fix reference contains empty versus per-atom quantities. If the fix reference contains empty
brackets, then per-atom values calculated by the fix are accessed. brackets, then per-atom values calculated by the fix are accessed.
Otherwise a single value (global or per-atom) calculated by the Otherwise a single value (global or per-atom) calculated by the fix is
fix is accessed. accessed.
Note that some fixes only generate quantities on certain timesteps. Note that some fixes only generate quantities on certain timesteps.
If a variable attempts to access the fix on non-allowed timesteps, an If a variable attempts to access the fix on non-allowed timesteps, an
error is generated. For example, the "fix ave/time"_fix_ave_time.html error is generated. For example, the "fix ave/time"_fix_ave_time.html
command may only generate averaged quantities every 100 steps. See command may only generate averaged quantities every 100 steps. See
the doc pages for individual fix commands for details. the doc pages for individual fix commands for details. If a variable
containing a fix is evaluated in an input script (not during a run),
then the values accessed by the fix should be current. See the
discussion below about "Variable Accuracy".
The different kinds of fix references are exactly the same as the The different kinds of fix references are exactly the same as the
compute references listed in the above table, where "c_" is replaced compute references listed in the above table, where "c_" is replaced
@ -349,47 +372,176 @@ then LAMMPS will run for a while when the print statement is invoked!
:line :line
It is useful to understand the distinction between referencing a Immediate Evaluation of Variables:
variable in a formula using the $x form instead of v_x. There is a
subtle difference between the two references that has to do with when
the evaluation of the included variable is done.
Referencing the variable as $x, the value of the include variable is There is a difference between referencing a variable with a leading $
substituted for immediately when the line is read from the input sign (e.g. $x or $\{abc\}) versus with a leading "v_" (e.g. v_x or
script, just as it would be in other input script command. v_abc). The former can be used in any command, including a variable
command, to force the immediate evaluation of the referenced variable
and the substitution of its value into the command. The latter is a
required kind of argument to some commands (e.g. the "fix
ave/spatial"_fix_ave_spatial.html or "dump custom"_dump.html or
"thermo_style"_thermo_style.html commands) if you wish it to evaluate
a variable periodically during a run. It can also be used in a
variable formula if you wish to reference a second variable. The
second variable will be evaluated whenever the first variable is
evaluated.
This could be the desired behavior if a static value is desired. Or As an example, suppose you use this command in your input script to
it could be the desired behavior for an equal-style variable if the define the variable "v" as
variable command appears in a loop (see the "jump"_jump.html and
"next"_next.html commands), since the substitution will be performed
anew each time thru the loop as the command is re-read. Note that if
the variable formula is enclosed in double quotes, this prevents
variable substitution and thus an error will be generated when the
variable formula is evaluated.
Referencing the variable as v_x, the value of the included variable variable v equal vol :pre
will not be accessed until the variable formula is evaluated. Thus
the value may change each time the evaluation is performed. This may
also be desired behavior.
As an example, if the current simulation box volume is 1000.0, then before a run where the simulation box size changes. You might think
these lines: this will assign the initial volume to the variable "v". That is not
the case. Rather it assigns a formula which evaluates the volume
(using the thermo_style keyword "vol") to the variable "v". If you
use the variable "v" in some other command like "fix ave/time" then
the current volume of the box will be evaluated continuously during
the run.
variable x equal vol If you want to store the initial volume of the system, you can do it
variable y equal 2*$x :pre this way:
will associate the equation string "2*1000.0" with variable y. variable v equal vol
variable v0 equal $v :pre
By contrast, these lines: The second command will force "v" to be evaluated (yielding the
initial volume) and assign that value to the variable "v0". Thus the
command
variable x equal vol thermo_style custom step v_v v_v0 :pre
variable y equal 2*v_x :pre
will associate the equation string "2*v_x" with variable y. would print out both the current and initial volume periodically
during the run.
Thus if the variable y were evaluated periodically during a run where Note that it is a mistake to enclose a variable formula in double
the box volume changed, the resulting value would always be 2000.0 for quotes if it contains variables preceeded by $ signs. For example,
the first case, but would change dynamically for the second case.
variable vratio equal "$\{vfinal\}/$\{v0\}" :pre
This is because the quotes prevent variable substitution (see "this
section"_Section_commands.html#3_2 on parsing input script commands),
and thus an error will occur when the formula for "vratio" is
evaluated later.
:line
Variable Accuracy:
Obviously, LAMMPS attempts to evaluate variables containing formulas
({equal} and {atom} style variables) accurately whenever the
evaluation is performed. Depending on what is included in the
formula, this may require invoking a "compute"_compute.html, either
directly or indirectly via a thermo keyword, or accessing a value
calculated and stored by a "fix"_fix.html. If the compute is one that
calculates the pressure or energy of the system, then these quantities
need to be tallied during the evaluation of the interatomic potentials
(pair, bond, etc) on timesteps that the variable will need the values.
LAMMPS keeps track of all of this during a "run"_run.html or "energy
minimization"_minimize.html. An error will be generated if you
attempt to evaluate a variable on timesteps when it cannot produce
accurate values. For example, if a "thermo_style
custom"_thermo_style.html command prints a variable which accesses
values stored by a "fix ave/time"_fix_ave_time.html command and the
timesteps on which thermo output is generated are not multiples of the
averaging frequency used in the fix command, then it is an error.
However, your input script can also require variables to be evaluated
before or after or inbetween runs. In this case, one of three things
may happen.
(1) The variable may be evaluated accurately. If it contains
references to a compute or fix, and these values were calculated and
stored on the last timestep of a preceeding run, then they can be
accessed and used by the variable.
(2) LAMMPS may not be able to evaluate the variable and generate an
error. For example, if the variable formula requires a
"compute"_compute.html to be invoked, either directly or indirectly
via a thermo keyword, then the variable cannot be evaluated before the
first run has occurred. The general rule is that if a variable uses a
value calculated by a compute, and the variable is not being evaluated
during a run, then the variable will not invoke the compute. Instead,
it can only use the value stored by the compute, which for accuracy
requires that the compute was already invoked on the same timestep
during a preceeding run.
Thus the way to get around this error is to perform a 0-timestep run
before using the variable. For example, these commands
variable t equal temp
print "Initial temperature = $t"
run 1000 :pre
will generate an error if the run is the first run specified in the
input script, because generating a value for the "t" variable requires
a compute for calculating the temperature to be invoked.
However, this sequence of commands would be fine:
run 0
variable t equal temp
print "Initial temperature = $t"
run 1000 :pre
The 0-timestep run initializes and invokes various computes, including
the one for temperature, so that the value it stores is current and
can be accessed by the variable "t" after the run has completed. Note
that a 0-timestep run does not alter the state of the system, so it
does not change the input state for the 1000-timestep run that
follows. Also note, that the 0-timestep run must actually use and
invoke the compute in question (e.g. via "thermo"_thermo_style.html or
"dump"_dump.html output) in order for it to enable the compute to be
used in a variable after the run.
Note that unlike computes, "fixes"_fix.html will never generate an
error if their values are accessed by a variable in between runs.
They always return some value to the variable. However, this value
may not be what you expect if the fix has not yet calculated the
quantity of interest. For example, the "fix indent"_fix_indent.html
command stores the force on the indenter. But this is not computed
until a run is performed. Thus if a variable attempts to print this
value before the first run, values of zero will be output. Again,
performing a 0-timestep run before printing the variable has the
desired effect.
(3) The variable may be evaluated incorrectly. And LAMMPS may have
no way to detect this has occurred. Consider the following sequence
of commands:
pair_coeff 1 1 1.0 1.0
run 1000
pair_coeff 1 1 1.5 1.0
variable e equal pe
print "Final potential energy = $e" :pre
The first run is performed using one setting for the pairwise
potential defined by the "pair_style"_pair_style.html and
"pair_coeff"_pair_coeff.html commands. The potential energy is
evaluated on the final timestep and stored by the "compute
pe"_compute_pe.html compute (this is done by the
"thermo_style"_thermo_style.html command). Then a pair coefficient is
changed, altering the potential energy of the system. When the
potential energy is printed via the "e" variable, LAMMPS will use the
potential energy value stored by the "compute pe"_compute_pe.html
compute, thinking it is current. There are many other commands which
could alter the state of the system between runs, causing a variable
to evaluate incorrectly.
The solution to this issue is the same as for case (2) above, namely
to perform a 0-timestep run before the variable is evaluated to insure
the system is up-to-date. For example, this sequence of commands
would print a potential energy that reflected the changed pairwise
coefficient:
pair_coeff 1 1 1.0 1.0
run 1000
pair_coeff 1 1 1.5 1.0
run 0
variable e equal pe
print "Final potential energy = $e" :pre
:line :line