git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1733 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_nph.html

@@ -125,8 +125,10 @@ Typically a value between 0.2 to 2.0 is sufficient to damp
 oscillations after a few periods.
 </P>
 <P>For all pressure styles, the simulation box stays rectangular in
-shape.  Parinello-Rahman boundary conditions (tilted box) for this fix
-are not yet implemented in LAMMPS.
+shape.  Parinello-Rahman boundary condition for tilted boxes
+(triclinic symmetry) are supported by other LAMMPS commands (see <A HREF = "Section_howto.html#4_12">this
+section</A> of the manual), but not yet by this
+command.
 </P>
 <P>For all styles, the <I>Pdamp</I> parameter determines the time scale on
 which pressure is relaxed.  For example, a value of 1000.0 means to

doc/fix_nph.txt

@@ -116,8 +116,10 @@ Typically a value between 0.2 to 2.0 is sufficient to damp
 oscillations after a few periods.
 
 For all pressure styles, the simulation box stays rectangular in
-shape.  Parinello-Rahman boundary conditions (tilted box) for this fix
-are not yet implemented in LAMMPS.
+shape.  Parinello-Rahman boundary condition for tilted boxes
+(triclinic symmetry) are supported by other LAMMPS commands (see "this
+section"_Section_howto.html#4_12 of the manual), but not yet by this
+command.
 
 For all styles, the {Pdamp} parameter determines the time scale on
 which pressure is relaxed.  For example, a value of 1000.0 means to

doc/fix_npt.html

@@ -136,8 +136,10 @@ is working.  Typically a value between 0.2 to 2.0 is sufficient to
 damp oscillations after a few periods.
 </P>
 <P>For all pressure styles, the simulation box stays rectangular in
-shape.  Parinello-Rahman boundary conditions (tilted box) for this fix
-are not yet implemented in LAMMPS.
+shape.  Parinello-Rahman boundary condition for tilted boxes
+(triclinic symmetry) are supported by other LAMMPS commands (see <A HREF = "Section_howto.html#4_12">this
+section</A> of the manual), but not yet by this
+command.
 </P>
 <P>For all styles, the <I>Pdamp</I> parameter operates like the <I>Tdamp</I>
 parameter, determining the time scale on which pressure is relaxed.

doc/fix_npt.txt

@@ -125,8 +125,10 @@ is working.  Typically a value between 0.2 to 2.0 is sufficient to
 damp oscillations after a few periods.
 
 For all pressure styles, the simulation box stays rectangular in
-shape.  Parinello-Rahman boundary conditions (tilted box) for this fix
-are not yet implemented in LAMMPS.
+shape.  Parinello-Rahman boundary condition for tilted boxes
+(triclinic symmetry) are supported by other LAMMPS commands (see "this
+section"_Section_howto.html#4_12 of the manual), but not yet by this
+command.
 
 For all styles, the {Pdamp} parameter operates like the {Tdamp}
 parameter, determining the time scale on which pressure is relaxed.

doc/fix_press_berendsen.html

@@ -117,8 +117,10 @@ Typically a value between 0.2 to 2.0 is sufficient to damp
 oscillations after a few periods.
 </P>
 <P>For all pressure styles, the simulation box stays rectangular in
-shape.  Parinello-Rahman boundary conditions (tilted box) for this fix
-are not yet implemented in LAMMPS.
+shape.  Parinello-Rahman boundary condition for tilted boxes
+(triclinic symmetry) are supported by other LAMMPS commands (see <A HREF = "Section_howto.html#4_12">this
+section</A> of the manual), but not yet by this
+command.
 </P>
 <P>For all styles, the <I>Pdamp</I> parameter determines the time scale on
 which pressure is relaxed.  For example, a value of 1000.0 means to

doc/fix_press_berendsen.txt

@@ -108,8 +108,10 @@ Typically a value between 0.2 to 2.0 is sufficient to damp
 oscillations after a few periods.
 
 For all pressure styles, the simulation box stays rectangular in
-shape.  Parinello-Rahman boundary conditions (tilted box) for this fix
-are not yet implemented in LAMMPS.
+shape.  Parinello-Rahman boundary condition for tilted boxes
+(triclinic symmetry) are supported by other LAMMPS commands (see "this
+section"_Section_howto.html#4_12 of the manual), but not yet by this
+command.
 
 For all styles, the {Pdamp} parameter determines the time scale on
 which pressure is relaxed.  For example, a value of 1000.0 means to

doc/units.html

@@ -34,44 +34,51 @@ of an input script.
 www.physics.nist.gov. For the definition of Kcal in real units, LAMMPS
 uses the thermochemical calorie = 4.184 J.
 </P>
-<P>For style <I>lj</I>, all quantities are unitless:
+<P>For style <I>lj</I>, all quantities are unitless.  The formula relating the
+reduced or unitless quantity (with an asterisk) to the same quantity
+with units is also given:
 </P>
-<UL><LI>distance = sigma
-<LI>time = tau
-<LI>mass = one
-<LI>energy = epsilon
-<LI>velocity = sigma/tau
-<LI>force = epsilon/sigma
-<LI>temperature = reduced LJ temperature
-<LI>pressure = reduced LJ pressure
-<LI>charge = reduced LJ charge
-<LI>dipole = reduced LJ dipole moment
-<LI>electric field = force/charge 
+<UL><LI>m (mass) = epsilon = sigma = tau = Boltzmann constant = 1
+<LI>distance = sigma, where x* = x / sigma
+<LI>time = tau, where tau = t* = t (Kb T / m / sigma^2)^1/2
+<LI>energy = epsilon, where E* = E / epsilon
+<LI>velocity = sigma/tau, where v* = v tau / sigma
+<LI>force = epsilon/sigma, where f* = f sigma / epsilon
+<LI>temperature = reduced LJ temperature, where T* = T Kb / epsilon
+<LI>pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon
+<LI>viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau
+<LI>charge = reduced LJ charge, where q* = q / (4 pi perm0 sigma epsilon)^1/2
+<LI>dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2
+<LI>electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon 
 </UL>
 <P>For style <I>real</I>, these are the units:
 </P>
-<UL><LI>distance = Angstroms
-<LI>time = femtoseconds
+<UL><LI>Boltzmann constant = 0.0019872067 Kcal/mole per degree K
 <LI>mass = grams/mole
+<LI>distance = Angstroms
+<LI>time = femtoseconds
 <LI>energy = Kcal/mole 
 <LI>velocity = Angstroms/femtosecond 
 <LI>force = Kcal/mole-Angstrom
 <LI>temperature = degrees K
 <LI>pressure = atmospheres
+<LI>viscosity = Poise
 <LI>charge = multiple of electron charge (+1.0 is a proton)
 <LI>dipole = charge*Angstroms
 <LI>electric field = volts/Angstrom 
 </UL>
 <P>For style <I>metal</I>, these are the units:
 </P>
-<UL><LI>distance = Angstroms
-<LI>time = picoseconds
+<UL><LI>Boltzmann constant = 8.617343e-5 eV per degree K
 <LI>mass = grams/mole
+<LI>distance = Angstroms
+<LI>time = picoseconds
 <LI>energy = eV
 <LI>velocity = Angstroms/picosecond 
 <LI>force = eV/Angstrom
 <LI>temperature = degrees K
 <LI>pressure = bars
+<LI>viscosity = Poise
 <LI>charge = multiple of electron charge (+1.0 is a proton)
 <LI>dipole = charge*Angstroms
 <LI>electric field = volts/Angstrom 

doc/units.txt

@@ -31,44 +31,51 @@ For real and metallic units, LAMMPS uses physical constants from
 www.physics.nist.gov. For the definition of Kcal in real units, LAMMPS
 uses the thermochemical calorie = 4.184 J.
 
-For style {lj}, all quantities are unitless:
+For style {lj}, all quantities are unitless.  The formula relating the
+reduced or unitless quantity (with an asterisk) to the same quantity
+with units is also given:
 
-distance = sigma
-time = tau
-mass = one
-energy = epsilon
-velocity = sigma/tau
-force = epsilon/sigma
-temperature = reduced LJ temperature
-pressure = reduced LJ pressure
-charge = reduced LJ charge
-dipole = reduced LJ dipole moment
-electric field = force/charge :ul
+m (mass) = epsilon = sigma = tau = Boltzmann constant = 1
+distance = sigma, where x* = x / sigma
+time = tau, where tau = t* = t (Kb T / m / sigma^2)^1/2
+energy = epsilon, where E* = E / epsilon
+velocity = sigma/tau, where v* = v tau / sigma
+force = epsilon/sigma, where f* = f sigma / epsilon
+temperature = reduced LJ temperature, where T* = T Kb / epsilon
+pressure = reduced LJ pressure, where P* = P sigma^3 / epsilon
+viscosity = reduced LJ viscosity, where eta* = eta sigma^3 / epsilon / tau
+charge = reduced LJ charge, where q* = q / (4 pi perm0 sigma epsilon)^1/2
+dipole = reduced LJ dipole, moment where *mu = mu / (4 pi perm0 sigma^3 epsilon)^1/2
+electric field = force/charge, where E* = E (4 pi perm0 sigma epsilon)^1/2 sigma / epsilon :ul
 
 For style {real}, these are the units:
 
+Boltzmann constant = 0.0019872067 Kcal/mole per degree K
+mass = grams/mole
 distance = Angstroms
 time = femtoseconds
-mass = grams/mole
 energy = Kcal/mole 
 velocity = Angstroms/femtosecond 
 force = Kcal/mole-Angstrom
 temperature = degrees K
 pressure = atmospheres
+viscosity = Poise
 charge = multiple of electron charge (+1.0 is a proton)
 dipole = charge*Angstroms
 electric field = volts/Angstrom :ul
 
 For style {metal}, these are the units:
 
+Boltzmann constant = 8.617343e-5 eV per degree K
+mass = grams/mole
 distance = Angstroms
 time = picoseconds
-mass = grams/mole
 energy = eV
 velocity = Angstroms/picosecond 
 force = eV/Angstrom
 temperature = degrees K
 pressure = bars
+viscosity = Poise
 charge = multiple of electron charge (+1.0 is a proton)
 dipole = charge*Angstroms
 electric field = volts/Angstrom :ul