diff --git a/doc/html/Section_commands.html b/doc/html/Section_commands.html index 232a285c69..999710b03a 100644 --- a/doc/html/Section_commands.html +++ b/doc/html/Section_commands.html @@ -1183,9 +1183,9 @@ if + - awpmd/cut @@ -1224,29 +1224,29 @@ if mgpt morse/smooth/linear +morse/soft multi/lucy quip -reax/c -smd/hertz +reax/c +smd/hertz smd/tlsph smd/triangulated/surface -smd/ulsph -smtbq +smd/ulsph +smtbq sph/heatconduction sph/idealgas -sph/lj -sph/rhosum +sph/lj +sph/rhosum sph/taitwater sph/taitwater/morris -srp -tersoff/table (o) +srp +tersoff/table (o) thole tip4p/long/soft (o) -  diff --git a/doc/html/_sources/Section_commands.txt b/doc/html/_sources/Section_commands.txt index f94764a1c9..f19aa4047c 100644 --- a/doc/html/_sources/Section_commands.txt +++ b/doc/html/_sources/Section_commands.txt @@ -648,31 +648,31 @@ KOKKOS, o = USER-OMP, t = OPT. These are additional pair styles in USER packages, which can be used if :ref:`LAMMPS is built with the appropriate package `. -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`awpmd/cut ` | :doc:`buck/mdf ` | :doc:`coul/cut/soft (o) ` | :doc:`coul/diel (o) ` | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`coul/long/soft (o) ` | :doc:`dpd/fdt ` | :doc:`dpd/fdt/energy ` | :doc:`eam/cd (o) ` | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`edip (o) ` | :doc:`eff/cut ` | :doc:`gauss/cut ` | :doc:`lennard/mdf ` | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`list ` | :doc:`lj/charmm/coul/long/soft (o) ` | :doc:`lj/cut/coul/cut/soft (o) ` | :doc:`lj/cut/coul/long/soft (o) ` | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`lj/cut/dipole/sf (go) ` | :doc:`lj/cut/soft (o) ` | :doc:`lj/cut/thole/long (o) ` | :doc:`lj/cut/tip4p/long/soft (o) ` | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`lj/mdf ` | :doc:`lj/sdk (gko) ` | :doc:`lj/sdk/coul/long (go) ` | :doc:`lj/sdk/coul/msm (o) ` | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`lj/sf (o) ` | :doc:`meam/spline ` | :doc:`meam/sw/spline ` | :doc:`mgpt ` | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`morse/smooth/linear ` | :doc:`multi/lucy ` | :doc:`quip ` | :doc:`reax/c ` | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`smd/hertz ` | :doc:`smd/tlsph ` | :doc:`smd/triangulated/surface ` | :doc:`smd/ulsph ` | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`smtbq ` | :doc:`sph/heatconduction ` | :doc:`sph/idealgas ` | :doc:`sph/lj ` | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`sph/rhosum ` | :doc:`sph/taitwater ` | :doc:`sph/taitwater/morris ` | :doc:`srp ` | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ -| :doc:`tersoff/table (o) ` | :doc:`thole ` | :doc:`tip4p/long/soft (o) ` | | -+--------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+--------------------------------------------------+ ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`awpmd/cut ` | :doc:`buck/mdf ` | :doc:`coul/cut/soft (o) ` | :doc:`coul/diel (o) ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`coul/long/soft (o) ` | :doc:`dpd/fdt ` | :doc:`dpd/fdt/energy ` | :doc:`eam/cd (o) ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`edip (o) ` | :doc:`eff/cut ` | :doc:`gauss/cut ` | :doc:`lennard/mdf ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`list ` | :doc:`lj/charmm/coul/long/soft (o) ` | :doc:`lj/cut/coul/cut/soft (o) ` | :doc:`lj/cut/coul/long/soft (o) ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`lj/cut/dipole/sf (go) ` | :doc:`lj/cut/soft (o) ` | :doc:`lj/cut/thole/long (o) ` | :doc:`lj/cut/tip4p/long/soft (o) ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`lj/mdf ` | :doc:`lj/sdk (gko) ` | :doc:`lj/sdk/coul/long (go) ` | :doc:`lj/sdk/coul/msm (o) ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`lj/sf (o) ` | :doc:`meam/spline ` | :doc:`meam/sw/spline ` | :doc:`mgpt ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`morse/smooth/linear ` | :doc:`morse/soft ` | :doc:`multi/lucy ` | :doc:`quip ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`reax/c ` | :doc:`smd/hertz ` | :doc:`smd/tlsph ` | :doc:`smd/triangulated/surface ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`smd/ulsph ` | :doc:`smtbq ` | :doc:`sph/heatconduction ` | :doc:`sph/idealgas ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`sph/lj ` | :doc:`sph/rhosum ` | :doc:`sph/taitwater ` | :doc:`sph/taitwater/morris ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ +| :doc:`srp ` | :doc:`tersoff/table (o) ` | :doc:`thole ` | :doc:`tip4p/long/soft (o) ` | ++--------------------------------------------+---------------------------------------------------+-----------------------------------------------------+-----------------------------------------------------------------+ ---------- diff --git a/doc/html/_sources/compute_fep.txt b/doc/html/_sources/compute_fep.txt index ab8925898c..6da9e144a5 100644 --- a/doc/html/_sources/compute_fep.txt +++ b/doc/html/_sources/compute_fep.txt @@ -61,15 +61,15 @@ thermodynamic integration (FDTI) or Bennet's acceptance ratio method The potential energy of the system is decomposed in three terms: a background term corresponding to interaction sites whose parameters -remain constant, a reference term *U*\ 0 corresponding to the +remain constant, a reference term :math:`U_0` corresponding to the initial interactions of the atoms that will undergo perturbation, and -a term *U*\ 1 corresponding to the final interactions of +a term :math:`U_1` corresponding to the final interactions of these atoms: .. image:: Eqs/compute_fep_u.jpg :align: center -A coupling parameter λ varying from 0 to 1 connects the +A coupling parameter :math:`\lambda` varying from 0 to 1 connects the reference and perturbed systems: .. image:: Eqs/compute_fep_lambda.jpg @@ -79,7 +79,7 @@ It is possible but not necessary that the coupling parameter (or a function thereof) appears as a multiplication factor of the potential energy. Therefore, this compute can apply perturbations to interaction parameters that are not directly proportional to the potential energy -(e.g. σ in Lennard-Jones potentials). +(e.g. :math:`\sigma` in Lennard-Jones potentials). This command can be combined with :doc:`fix adapt ` to perform multistage free-energy perturbation calculations along @@ -91,26 +91,26 @@ stepwise alchemical transformations during a simulation run: This compute is suitable for the finite-difference thermodynamic integration (FDTI) method :ref:`(Mezei) `, which is based on an evaluation of the numerical derivative of the free energy by a -perturbation method using a very small δ: +perturbation method using a very small :math:`\delta`: .. image:: Eqs/compute_fep_fdti.jpg :align: center -where *w*\ i are weights of a numerical quadrature. The :doc:`fix adapt ` command can be used to define the stages of -λ at which the derivative is calculated and averaged. +where :math:`w_i` are weights of a numerical quadrature. The :doc:`fix adapt ` command can be used to define the stages of +:math:`\lambda` at which the derivative is calculated and averaged. The compute fep calculates the exponential Boltzmann term and also the -potential energy difference *U*\ 1-\ *U*\ 0. By -choosing a very small perturbation δ the thermodynamic +potential energy difference :math:`U_1 -U_0`. By +choosing a very small perturbation :math:`\delta` the thermodynamic integration method can be implemented using a numerical evaluation of -the derivative of the potential energy with respect to λ: +the derivative of the potential energy with respect to :math:`\lambda`: .. image:: Eqs/compute_fep_ti.jpg :align: center Another technique to calculate free energy differences is the acceptance ratio method :ref:`(Bennet) `, which can be implemented -by calculating the potential energy differences with δ = 1.0 on +by calculating the potential energy differences with :math:`\delta` = 1.0 on both the forward and reverse routes: .. image:: Eqs/compute_fep_bar.jpg @@ -241,12 +241,12 @@ trajectories during which the volume fluctuates or changes :ref:`(Allen and Tild **Output info:** This compute calculates a global vector of length 3 which contains the -energy difference (\ *U*\ 1-\ *U*\ 0) as c_ID[1], the -Boltzmann factor exp(-(\ *U*\ 1-\ *U*\ 0)/\ *kT*\ ), or -*V*\ exp(-(\ *U*\ 1-\ *U*\ 0)/\ *kT*\ ), as c_ID[2] and the -volume of the simulation box *V* as c_ID[3]. *U*\ 1 is the +energy difference ( :math:`U_1-U_0` ) as c_ID[1], the +Boltzmann factor :math:`\exp(-(U_1-U_0)/kT)`, or +:math:`V \exp(-(U_1-U_0)/kT)`, as c_ID[2] and the +volume of the simulation box :math:`V` as c_ID[3]. :math:`U_1` is the pair potential energy obtained with the perturbed parameters and -*U*\ 0 is the pair potential energy obtained with the +:math:`U_0` is the pair potential energy obtained with the unperturbed parameters. The energies include kspace terms if these are used in the simulation. diff --git a/doc/html/_sources/compute_voronoi_atom.txt b/doc/html/_sources/compute_voronoi_atom.txt index d6b0efea82..b61dff650d 100644 --- a/doc/html/_sources/compute_voronoi_atom.txt +++ b/doc/html/_sources/compute_voronoi_atom.txt @@ -44,12 +44,8 @@ Examples compute 2 precipitate voronoi/atom surface matrix compute 3b precipitate voronoi/atom radius v_r compute 4 solute voronoi/atom only_group - -.. parsed-literal:: - compute 5 defects voronoi/atom occupation - -compute 6 all voronoi/atom neighbors yes + compute 6 all voronoi/atom neighbors yes Description """"""""""" diff --git a/doc/html/_sources/fix_lb_rigid_pc_sphere.txt b/doc/html/_sources/fix_lb_rigid_pc_sphere.txt index 406d7e41b0..4d73349d76 100644 --- a/doc/html/_sources/fix_lb_rigid_pc_sphere.txt +++ b/doc/html/_sources/fix_lb_rigid_pc_sphere.txt @@ -89,7 +89,7 @@ Restart, fix_modify, output, run start/stop, minimize info No information about the *rigid* and *rigid/nve* fixes are written to :doc:`binary restart files `. -Similar to the :doc:`fix rigid ` command: " The rigid +Similar to the :doc:`fix rigid ` command: The rigid fix computes a global scalar which can be accessed by various :ref:`output commands `. The scalar value calculated by these fixes is "intensive". The scalar is the current temperature of the collection of rigid bodies. This is averaged over all rigid @@ -99,9 +99,9 @@ mass of the body and v = the velocity of its center of mass. The rotational energy of a rigid body is 1/2 I w^2, where I = the moment of inertia tensor of the body and w = its angular velocity. Degrees of freedom constrained by the *force* and *torque* keywords are -removed from this calculation." +removed from this calculation. -"All of these fixes compute a global array of values which can be +All of these fixes compute a global array of values which can be accessed by various :ref:`output commands `. The number of rows in the array is equal to the number of rigid bodies. The number of columns is 15. Thus for each rigid body, 15 @@ -125,7 +125,7 @@ they are independent of the number of atoms in the simulation. No parameter of these fixes can be used with the *start/stop* keywords of the :doc:`run ` command. These fixes are not invoked during -:doc:`energy minimization `. " +:doc:`energy minimization `. Restrictions """""""""""" diff --git a/doc/html/_sources/pair_coeff.txt b/doc/html/_sources/pair_coeff.txt index a4cd065d38..6c00391d9e 100644 --- a/doc/html/_sources/pair_coeff.txt +++ b/doc/html/_sources/pair_coeff.txt @@ -118,7 +118,7 @@ Windows: .. parsed-literal:: - % set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials" + % set LAMMPS_POTENTIALS="C:\\Path to LAMMPS\\Potentials" ---------- diff --git a/doc/html/_sources/pair_morse.txt b/doc/html/_sources/pair_morse.txt index 810af22422..02afa218c5 100644 --- a/doc/html/_sources/pair_morse.txt +++ b/doc/html/_sources/pair_morse.txt @@ -18,24 +18,43 @@ pair_style morse/smooth/linear command pair_style morse/smooth/linear/omp command ========================================== +pair_style morse/soft command +============================= + Syntax """""" .. parsed-literal:: - pair_style morse cutoff + pair_style style args -* cutoff = global cutoff for Morse interactions (distance units) +* style = *morse* or *morse/smooth/linear* or *morse/soft* +* args = list of arguments for a particular style + +.. parsed-literal:: + + *morse* args = cutoff + cutoff = global cutoff for Morse interactions (distance units) + *morse/smooth/linear* args = cutoff + cutoff = global cutoff for Morse interactions (distance units) + *morse/soft* args = n lf cutoff + n = soft-core parameter + lf = transformation range is lf < lambda < 1 + cutoff = global cutoff for Morse interactions (distance units) Examples """""""" +pair_style morse 2.5 +pair_style morse/smooth/linear 2.5 +pair_coeff * * 100.0 2.0 1.5 +pair_coeff 1 1 100.0 2.0 1.5 3.0 + .. parsed-literal:: - pair_style morse 2.5 - pair_style morse/smooth/linear 2.5 - pair_coeff * * 100.0 2.0 1.5 - pair_coeff 1 1 100.0 2.0 1.5 3.0 + pair_style morse/soft 4 0.9 10.0 + pair_coeff * * 100.0 2.0 1.5 1.0 + pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 Description """"""""""" @@ -58,16 +77,16 @@ commands: * r0 (distance units) * cutoff (distance units) -* The last coefficient is optional. If not specified, the global morse -* cutoff is used. +The last coefficient is optional. If not specified, the global morse +cutoff is used. ---------- -The *smooth/linear* variant is similar to the lj/smooth/linear variant -in that it adds to the potential a shift and a linear term to make both -the potential energy and force go to zero at the cut-off: +The *morse/smooth/linear* variant is similar to the lj/smooth/linear +variant in that it adds to the potential a shift and a linear term +so that both, potential energy and force, go to zero at the cut-off: .. image:: Eqs/pair_morse_smooth_linear.jpg :align: center @@ -79,6 +98,30 @@ the *morse* and *morse/smooth/linear* styles. ---------- +The *morse/soft* variant is similar to the *lj/cut/soft* pair style +in that it modifies the potential at short range to have a soft core. +This helps to avoid singularities during free energy calculation in +which sites are created or anihilated. The formula differs from that +of *lj/cut/soft*\ , and is instead given by: + +.. image:: Eqs/pair_morse_soft.jpg + :align: center + +The *morse/soft* style requires the following pair coefficients: + +* D0 (energy units) +* alpha (1/distance units) +* r0 (distance units) +* lamda (unitless, between 0.0 and 1.0) +* cutoff (distance units) + +The last coefficient is optional. If not specified, the global morse +cutoff is used. + + +---------- + + Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -135,6 +178,9 @@ Restrictions The *morse/smooth/linear* pair style is only enabled if LAMMPS was built with the USER-MISC package. See the :ref:`Making LAMMPS ` section for more info. +The *morse/soft* pair style is only enabled if LAMMPS was built with +the USER-FEP package. See the :ref:`Making LAMMPS ` section for more info. + Related commands """""""""""""""" diff --git a/doc/html/_sources/tutorial_drude.txt b/doc/html/_sources/tutorial_drude.txt index fb1865b886..4a72b8d157 100644 --- a/doc/html/_sources/tutorial_drude.txt +++ b/doc/html/_sources/tutorial_drude.txt @@ -27,23 +27,11 @@ stiffness of the harmonic bond should be large, so that the Drude particle remains close ot the core. The values of Drude mass, Drude charge, and force constant can be chosen following different strategies, as in the following examples of polarizable force -fields. +fields: -* :ref:`Lamoureux and Roux ` suggest adopting a global - half-stiffness, :math:`K_D` = 500 kcal/(mol Å2) — - which corresponds to a force constant :math:`k_D` = 4184 kJ/(mol - Å2) — for all types of core-Drude bond, a - global mass :math:`m_D` = 0.4 g/mol (or u) for all types of Drude - particle, and to calculate the Drude charges for individual atom types - from the atom polarizabilities using equation (1). This choice is - followed in the polarizable CHARMM force field. -* :ref:`Schroeder and Steinhauser ` suggest adopting a global - charge :math:`q_D` = -1.0e and a global mass :math:`m_D` = 0.1 g/mol (or u) - for all Drude particles, and to calculate the force constant for each - type of core-Drude bond from equation (1). The timesteps used by these - authors are between 0.5 and 2 fs, with the degrees of freedom of the - Drude oscillators kept cold at 1 K. In both these force fields - hydrogen atoms are treated as non-polarizable. +#. :ref:`Lamoureux and Roux ` suggest adopting a global half-stiffness, :math:`K_D` = 500 kcal/(mol Ang :math:`{}^2`) - which corresponds to a force constant :math:`k_D` = 4184 kJ/(mol Ang :math:`{}^2`) - for all types of core-Drude bond, a global mass :math:`m_D` = 0.4 g/mol (or u) for all types of Drude particles, and to calculate the Drude charges for individual atom types from the atom polarizabilities using equation (1). This choice is followed in the polarizable CHARMM force field. +#. Alternately :ref:`Schroeder and Steinhauser ` suggest adopting a global charge :math:`q_D` = -1.0e and a global mass :math:`m_D` = 0.1 g/mol (or u) for all Drude particles, and to calculate the force constant for each type of core-Drude bond from equation (1). The timesteps used by these authors are between 0.5 and 2 fs, with the degrees of freedom of the Drude oscillators kept cold at 1 K. +#. In both these force fields hydrogen atoms are treated as non-polarizable. The motion of of the Drude particles can be calculated by minimizing the energy of the induced dipoles at each timestep, by an interative, self-consistent procedure. The Drude particles can be massless and @@ -67,17 +55,8 @@ are such that the core-shell model is sufficiently stable. But to be applicable to molecular/covalent systems the Drude model includes two important features: -#. The possibility to thermostat the additional degrees of freedom - associated with the induced dipoles at very low temperature, in terms - of the reduced coordinates of the Drude particles with respect to - their cores. This makes the trajectory close to that of relaxed - induced dipoles. -#. The Drude dipoles on covalently bonded atoms interact too strongly - due to the short distances, so an atom may capture the Drude particle - (shell) of a neighbor, or the induced dipoles within the same molecule - may align too much. To avoid this, damping at short of the - interactions between the point charges composing the induced dipole - can be done by :ref:`Thole ` functions. +#. The possibility to thermostat the additional degrees of freedom associated with the induced dipoles at very low temperature, in terms of the reduced coordinates of the Drude particles with respect to their cores. This makes the trajectory close to that of relaxed induced dipoles. +#. The Drude dipoles on covalently bonded atoms interact too strongly due to the short distances, so an atom may capture the Drude particle (shell) of a neighbor, or the induced dipoles within the same molecule may align too much. To avoid this, damping at short of the interactions between the point charges composing the induced dipole can be done by :ref:`Thole ` functions. ---------- @@ -483,7 +462,7 @@ NPT ensemble using Nose-Hoover thermostat: -**(Schroeder)** Schröder and Steinhauser, J Chem Phys, 133, +**(Schroeder)** Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010). .. _Jiang: diff --git a/doc/html/_sources/tutorial_github.txt b/doc/html/_sources/tutorial_github.txt index 3aa6d8ae2c..37cb6ffb5c 100644 --- a/doc/html/_sources/tutorial_github.txt +++ b/doc/html/_sources/tutorial_github.txt @@ -1,5 +1,5 @@ LAMMPS GitHub tutorial -###################### +********************** written by Stefan Paquay ======================== diff --git a/doc/html/_sources/variable.txt b/doc/html/_sources/variable.txt index bb95afd0b0..0a5d3321fe 100644 --- a/doc/html/_sources/variable.txt +++ b/doc/html/_sources/variable.txt @@ -46,7 +46,7 @@ Syntax constants = PI, version, on, off, true, false, yes, no thermo keywords = vol, ke, press, etc from :doc:`thermo_style ` math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y, - x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x + x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x) @@ -456,9 +456,7 @@ references, and references to other variables. +--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Thermo keywords | vol, pe, ebond, etc | +--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ -| Math operators | (), -x, x+y, x-y, x*y, x/y, x^y, x%y, | -+--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ -| Math operators | (), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x | +| Math operators | (), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x | +--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ | Math functions | sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) | +--------------------+------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/doc/html/compute_fep.html b/doc/html/compute_fep.html index 32338d1bfc..5a7910465c 100644 --- a/doc/html/compute_fep.html +++ b/doc/html/compute_fep.html @@ -180,19 +180,19 @@ thermodynamic integration (FDTI) or Bennet’s acceptance ratio method (BAR).

The potential energy of the system is decomposed in three terms: a background term corresponding to interaction sites whose parameters -remain constant, a reference term U<sub>0</sub> corresponding to the +remain constant, a reference term \(U_0\) corresponding to the initial interactions of the atoms that will undergo perturbation, and -a term U<sub>1</sub> corresponding to the final interactions of +a term \(U_1\) corresponding to the final interactions of these atoms:

_images/compute_fep_u.jpg -

A coupling parameter &lambda; varying from 0 to 1 connects the +

A coupling parameter \(\lambda\) varying from 0 to 1 connects the reference and perturbed systems:

_images/compute_fep_lambda.jpg

It is possible but not necessary that the coupling parameter (or a function thereof) appears as a multiplication factor of the potential energy. Therefore, this compute can apply perturbations to interaction parameters that are not directly proportional to the potential energy -(e.g. &sigma; in Lennard-Jones potentials).

+(e.g. \(\sigma\) in Lennard-Jones potentials).

This command can be combined with fix adapt to perform multistage free-energy perturbation calculations along stepwise alchemical transformations during a simulation run:

@@ -200,19 +200,19 @@ stepwise alchemical transformations during a simulation run:

This compute is suitable for the finite-difference thermodynamic integration (FDTI) method (Mezei), which is based on an evaluation of the numerical derivative of the free energy by a -perturbation method using a very small &delta;:

+perturbation method using a very small \(\delta\):

_images/compute_fep_fdti.jpg -

where w<sub>i</sub> are weights of a numerical quadrature. The fix adapt command can be used to define the stages of -&lambda; at which the derivative is calculated and averaged.

+

where \(w_i\) are weights of a numerical quadrature. The fix adapt command can be used to define the stages of +\(\lambda\) at which the derivative is calculated and averaged.

The compute fep calculates the exponential Boltzmann term and also the -potential energy difference U<sub>1</sub>-U<sub>0</sub>. By -choosing a very small perturbation &delta; the thermodynamic +potential energy difference \(U_1 -U_0\). By +choosing a very small perturbation \(\delta\) the thermodynamic integration method can be implemented using a numerical evaluation of -the derivative of the potential energy with respect to &lambda;:

+the derivative of the potential energy with respect to \(\lambda\):

_images/compute_fep_ti.jpg

Another technique to calculate free energy differences is the acceptance ratio method (Bennet), which can be implemented -by calculating the potential energy differences with &delta; = 1.0 on +by calculating the potential energy differences with \(\delta\) = 1.0 on both the forward and reverse routes:

_images/compute_fep_bar.jpg

The value of the free energy difference is determined by numerical @@ -346,12 +346,12 @@ trajectories during which the volume fluctuates or changes

Output info:

This compute calculates a global vector of length 3 which contains the -energy difference (U<sub>1</sub>-U<sub>0</sub>) as c_ID[1], the -Boltzmann factor exp(-(U<sub>1</sub>-U<sub>0</sub>)/kT), or -Vexp(-(U<sub>1</sub>-U<sub>0</sub>)/kT), as c_ID[2] and the -volume of the simulation box V as c_ID[3]. U<sub>1</sub> is the +energy difference ( \(U_1-U_0\) ) as c_ID[1], the +Boltzmann factor \(\exp(-(U_1-U_0)/kT)\), or +\(V \exp(-(U_1-U_0)/kT)\), as c_ID[2] and the +volume of the simulation box \(V\) as c_ID[3]. \(U_1\) is the pair potential energy obtained with the perturbed parameters and -U<sub>0</sub> is the pair potential energy obtained with the +\(U_0\) is the pair potential energy obtained with the unperturbed parameters. The energies include kspace terms if these are used in the simulation.

These output results can be used by any command that uses a global diff --git a/doc/html/compute_voronoi_atom.html b/doc/html/compute_voronoi_atom.html index 5b05cb77a6..630ee3bac6 100644 --- a/doc/html/compute_voronoi_atom.html +++ b/doc/html/compute_voronoi_atom.html @@ -162,12 +162,10 @@ or face_threshold or neighbors or peratom compute 2 precipitate voronoi/atom surface matrix compute 3b precipitate voronoi/atom radius v_r compute 4 solute voronoi/atom only_group +compute 5 defects voronoi/atom occupation +compute 6 all voronoi/atom neighbors yes -

compute 5 defects voronoi/atom occupation
-
-
-

compute 6 all voronoi/atom neighbors yes

Description

diff --git a/doc/html/fix_lb_rigid_pc_sphere.html b/doc/html/fix_lb_rigid_pc_sphere.html index 2c21674c50..984513a2c2 100644 --- a/doc/html/fix_lb_rigid_pc_sphere.html +++ b/doc/html/fix_lb_rigid_pc_sphere.html @@ -176,7 +176,7 @@ created to be used in place of that fix, to integrate the equations of motion of spherical rigid bodies when a lattice-Boltzmann fluid is present with a user-specified value of the force-coupling constant. -The fix uses the integration algorithm described in Mackay et al. to update the positions, velocities, and orientations of +The fix uses the integration algorithm described in Mackay et al. to update the positions, velocities, and orientations of a set of spherical rigid bodies experiencing velocity dependent hydrodynamic forces. The spherical bodies are assumed to rotate as solid, uniform density spheres, with moments of inertia calculated @@ -207,7 +207,7 @@ assumes the constituent atoms are point particles); see

Restart, fix_modify, output, run start/stop, minimize info

No information about the rigid and rigid/nve fixes are written to binary restart files.

-

Similar to the fix rigid command: &quot; The rigid +

Similar to the fix rigid command: The rigid fix computes a global scalar which can be accessed by various output commands. The scalar value calculated by these fixes is “intensive”. The scalar is the current temperature of the collection of rigid bodies. This is averaged over all rigid @@ -217,8 +217,8 @@ mass of the body and v = the velocity of its center of mass. The rotational energy of a rigid body is 1/2 I w^2, where I = the moment of inertia tensor of the body and w = its angular velocity. Degrees of freedom constrained by the force and torque keywords are -removed from this calculation.&quot;

-

&quot;All of these fixes compute a global array of values which can be +removed from this calculation.

+

All of these fixes compute a global array of values which can be accessed by various output commands. The number of rows in the array is equal to the number of rigid bodies. The number of columns is 15. Thus for each rigid body, 15 @@ -239,7 +239,7 @@ of bodies.

they are independent of the number of atoms in the simulation.

No parameter of these fixes can be used with the start/stop keywords of the run command. These fixes are not invoked during -energy minimization. &quot;

+energy minimization.

Restrictions

diff --git a/doc/html/pair_coeff.html b/doc/html/pair_coeff.html index eac6bd4a7e..1689bf6047 100644 --- a/doc/html/pair_coeff.html +++ b/doc/html/pair_coeff.html @@ -223,7 +223,7 @@ for

Windows:

-% set LAMMPS_POTENTIALS="C:Path to LAMMPSPotentials"
+% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials"

The alphabetic list of pair styles defined in LAMMPS is given on the diff --git a/doc/html/pair_morse.html b/doc/html/pair_morse.html index 86eceae04c..bac9a4aa44 100644 --- a/doc/html/pair_morse.html +++ b/doc/html/pair_morse.html @@ -141,21 +141,38 @@

pair_style morse/smooth/linear/omp command

+
+
+

pair_style morse/soft command

Syntax

-
pair_style morse cutoff
+
pair_style style args
 

 

 
    
-
  • cutoff = global cutoff for Morse interactions (distance units)
    • 
+
  • style = morse or morse/smooth/linear or morse/soft
    • 
+
  • args = list of arguments for a particular style
    • 
 

+
+morse args = cutoff
+  cutoff = global cutoff for Morse interactions (distance units)
+morse/smooth/linear args = cutoff
+  cutoff = global cutoff for Morse interactions (distance units)
+morse/soft args = n lf cutoff
+  n = soft-core parameter
+  lf      = transformation range is lf < lambda < 1
+  cutoff  = global cutoff for Morse interactions (distance units)
+

Examples

-
pair_style morse 2.5
-pair_style morse/smooth/linear 2.5
-pair_coeff * * 100.0 2.0 1.5
-pair_coeff 1 1 100.0 2.0 1.5 3.0
+
pair_style morse 2.5
+pair_style morse/smooth/linear 2.5
+pair_coeff * * 100.0 2.0 1.5
+pair_coeff 1 1 100.0 2.0 1.5 3.0

+
pair_style morse/soft 4 0.9 10.0
+pair_coeff * * 100.0 2.0 1.5 1.0
+pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0
@@ -174,17 +191,34 @@ commands:

  • alpha (1/distance units)
  • r0 (distance units)
  • cutoff (distance units)
    • -
  • The last coefficient is optional. If not specified, the global morse
    • -
  • cutoff is used.
    • +

    The last coefficient is optional. If not specified, the global morse +cutoff is used.

    -

    The smooth/linear variant is similar to the lj/smooth/linear variant -in that it adds to the potential a shift and a linear term to make both -the potential energy and force go to zero at the cut-off:

    +

    The morse/smooth/linear variant is similar to the lj/smooth/linear +variant in that it adds to the potential a shift and a linear term +so that both, potential energy and force, go to zero at the cut-off:

    _images/pair_morse_smooth_linear.jpg

    The syntax of the pair_style and pair_coeff commands are the same for the morse and morse/smooth/linear styles.

    +

    The morse/soft variant is similar to the lj/cut/soft pair style +in that it modifies the potential at short range to have a soft core. +This helps to avoid singularities during free energy calculation in +which sites are created or anihilated. The formula differs from that +of lj/cut/soft, and is instead given by:

    +_images/pair_morse_soft.jpg +

    The morse/soft style requires the following pair coefficients:

    +
      +
    • D0 (energy units)
      • +
    • alpha (1/distance units)
      • +
    • r0 (distance units)
      • +
    • lamda (unitless, between 0.0 and 1.0)
      • +
    • cutoff (distance units)
      • +
    +

    The last coefficient is optional. If not specified, the global morse +cutoff is used.

    +

    Styles with a gpu, intel, kk, omp, or opt suffix are functionally the same as the corresponding style without the suffix. They have been optimized to run faster, depending on your available @@ -222,6 +256,8 @@ to be specified in an input script that reads a restart file.

    Restrictions

    The morse/smooth/linear pair style is only enabled if LAMMPS was built with the USER-MISC package. See the Making LAMMPS section for more info.

    +

    The morse/soft pair style is only enabled if LAMMPS was built with +the USER-FEP package. See the Making LAMMPS section for more info.

    (Lamoureux) Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003)

    -

    (Schroeder) Schr&ouml;der and Steinhauser, J Chem Phys, 133, +

    (Schroeder) Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010).

    (Jiang) Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,
    diff --git a/doc/html/tutorial_github.html b/doc/html/tutorial_github.html index 1071d78768..5f6c9e69ba 100644 --- a/doc/html/tutorial_github.html +++ b/doc/html/tutorial_github.html @@ -132,9 +132,11 @@

    This document briefly describes how to use GitHub to merge changes into LAMMPS using GitHub. It assumes that you are familiar with git. You may want to have a look at the Git book to reacquaint yourself.

    +
    +
    -

    Making an account

    +

    Making an account

    First of all, you need a GitHub account. This is fairly simple, just go to GitHub and create an account by clicking the ``Sign up for GitHub’’ button. Once your account is created, you @@ -143,7 +145,7 @@ username or e-mail address and password.

    -

    Forking the repository

    +

    Forking the repository

    To get changes into LAMMPS, you need to first fork the repository. At the time of writing, LAMMPS-ICMS is the preferred fork. Go to LAMMPS on GitHub and make sure branch is set to ``lammps-icms’‘, see the figure below.

    @@ -158,11 +160,9 @@ can include changes from upstream into your repository.

    -

    Adding changes to your own fork

    +

    Adding changes to your own fork

    Before adding changes, it is better to first create a new branch that will contain these changes, a so-called feature branch.

    -
    -

    Feature branches

    Since LAMMPS is such a big project and most user contributions come in @@ -210,6 +210,8 @@ $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt

    The “-m” switch is used to add a message to the commit. Use this to indicate what type of change was commited.

    +
    +

    Wisdom by Axel:

    “Do not use “git commit -a”. the -a flag will automatically include *all modified or new files. mercurial does that and it find it hugely annoying and often leading to accidental commits of files you @@ -260,16 +262,19 @@ is now up to the maintainer(s) of the upstream repository to incorporate the changes into the repository and to close the pull request.

    _images/tutorial_pull_request4.png +
    +
    +
    -

    Additional changes

    +

    Additional changes

    Before the pull request is accepted, any additional changes you push into your repository will automatically become part of the pull request.

    -

    After a merge

    +

    After a merge

    When everything is fine the feature branch is merged into the LAMMPS repositories:

    _images/tutorial_merged.png @@ -293,8 +298,6 @@ to your remote(s) as well:

    $ git push origin :add-user-manifold
    -
    - diff --git a/doc/html/variable.html b/doc/html/variable.html index f3fdbd8b64..1250ca06d3 100644 --- a/doc/html/variable.html +++ b/doc/html/variable.html @@ -168,7 +168,7 @@ constants = PI, version, on, off, true, false, yes, no thermo keywords = vol, ke, press, etc from thermo_style math operators = (), -x, x+y, x-y, x*y, x/y, x^y, x%y, - x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x + x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x math functions = sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x) @@ -536,36 +536,33 @@ references, and references to other variables.

    vol, pe, ebond, etc Math operators -(), -x, x+y, x-y, x*y, x/y, x^y, x%y, +(), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x < y, x <= y, x > y, x >= y, x && y, x || y, !x -Math operators -(), -x, x+y, x-y, x*y, x/y, x^y, x%y, x == y, x != y, x &lt y, x &lt= y, x &gt y, x &gt= y, x && y, x || y, !x - -Math functions +Math functions sqrt(x), exp(x), ln(x), log(x), abs(x), sin(x), cos(x), tan(x), asin(x), acos(x), atan(x), atan2(y,x), random(x,y,z), normal(x,y,z), ceil(x), floor(x), round(x), ramp(x,y), stagger(x,y), logfreq(x,y,z), logfreq2(x,y,z), stride(x,y,z), stride2(x,y,z,a,b,c), vdisplace(x,y), swiggle(x,y,z), cwiggle(x,y,z) -Group functions +Group functions count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID), ke(ID), angmom(ID,dim), torque(ID,dim), inertia(ID,dimdim), omega(ID,dim) -Region functions +Region functions count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) -Special functions +Special functions sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x) -Atom values +Atom values id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] -Atom vectors +Atom vectors id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q -Compute references +Compute references c_ID, c_ID[i], c_ID[i][j], C_ID, C_ID[i] -Fix references +Fix references f_ID, f_ID[i], f_ID[i][j], F_ID, F_ID[i] -Other variables +Other variables v_name, v_name[i]