diff --git a/doc/src/pair_meam.rst b/doc/src/pair_meam.rst index 022de60f98..afa89e10ca 100644 --- a/doc/src/pair_meam.rst +++ b/doc/src/pair_meam.rst @@ -75,16 +75,16 @@ N additional arguments after the second filename in the pair_coeff command, where N is the number of LAMMPS atom types: * MEAM library file -* Elem1, Elem2, ... +* Element1, Element2, ... * MEAM parameter file * N element names = mapping of MEAM elements to atom types See the :doc:`pair_coeff ` page for alternate ways to specify the path for the potential files. -As an example, the potentials/library.meam file has generic MEAM -settings for a variety of elements. The potentials/SiC.meam file has -specific parameter settings for a Si and C alloy system. If your +As an example, the ``potentials/library.meam`` file has generic MEAM +settings for a variety of elements. The ``potentials/SiC.meam`` file +has specific parameter settings for a Si and C alloy system. If your LAMMPS simulation has 4 atoms types and you want the first 3 to be Si, and the fourth to be C, you would use the following pair_coeff command: @@ -118,30 +118,30 @@ that will be used with other potentials. If the second filename is NULL, the element names between the two filenames can appear in any order, e.g. "Si C" or "C Si" in the - example above. However, if the second filename is not NULL (as in the - example above), it contains settings that are Fortran-indexed for the - elements that precede it. Thus you need to insure you list the - elements between the filenames in an order consistent with how the + example above. However, if the second filename is **not** NULL (as in the + example above), it contains settings that are indexed **by numbers** + for the elements that precede it. Thus you need to insure that you list + the elements between the filenames in an order consistent with how the values in the second filename are indexed. See details below on the syntax for settings in the second file. The MEAM library file provided with LAMMPS has the name -potentials/library.meam. It is the "meamf" file used by other MD -codes. Aside from blank and comment lines (start with #) which can -appear anywhere, it is formatted as a series of entries, each of which +``potentials/library.meam``. It is the "meamf" file used by other MD +codes. Aside from blank and comment lines (starting with # which can +appear anywhere), it is formatted as a series of entries, each of which has 19 parameters and can span multiple lines: elt, lat, z, ielement, atwt, alpha, b0, b1, b2, b3, alat, esub, asub, t0, t1, t2, t3, rozero, ibar -The "elt" and "lat" parameters are text strings, such as elt = Si or -Cu and lat = dia or fcc. Because the library file is used by Fortran +The *elt* and *lat* parameters are text strings, such as *elt* = Si or +Cu and *lat* = dia or fcc. Because the library file is used by Fortran MD codes, these strings may be enclosed in single quotes, but this is not required. The other numeric parameters match values in the -formulas above. The value of the "elt" string is what is used in the +formulas above. The value of the *elt* string is what is used in the pair_coeff command to identify which settings from the library file you wish to read in. There can be multiple entries in the library -file with the same "elt" value; LAMMPS reads the first matching entry it +file with the same *elt* value; LAMMPS reads the first matching entry it finds and ignores the rest. Other parameters in the MEAM library file correspond to single-element @@ -157,13 +157,13 @@ potential parameters: esub = energy per atom (eV) in the reference structure at equilibrium asub = "A" parameter for MEAM (see e.g. :ref:`(Baskes) `) -The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the +The *alpha*, *b0*, *b1*, *b2*, *b3*, *t0*, *t1*, *t2*, *t3* parameters correspond to the standard MEAM parameters in the literature :ref:`(Baskes) ` (the b parameters are the standard beta parameters). Note that only parameters -normalized to t0 = 1.0 are supported. The rozero parameter is +normalized to *t0 = 1.0* are supported. The *rozero* parameter is an element-dependent density scaling that weights the reference background density (see e.g. equation 4.5 in :ref:`(Gullet) `) and -is typically 1.0 for single-element systems. The ibar parameter +is typically 1.0 for single-element systems. The *ibar* parameter selects the form of the function G(Gamma) used to compute the electron density; options are @@ -180,7 +180,7 @@ If used, the MEAM parameter file contains settings that override or complement the library file settings. Examples of such parameter files are in the potentials directory with a ".meam" suffix. Their format is the same as is read by other Fortran MD codes. Aside from -blank and comment lines (start with #) which can appear anywhere, each +blank and comment lines (start with # which can appear anywhere), each line has one of the following forms. Each line can also have a trailing comment (starting with #) which is ignored. @@ -213,7 +213,7 @@ The recognized keywords for the parameter file are as follows: delta(I,J) = heat of formation for I-J alloy; if Ec_IJ is input as zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ alpha(I,J) = alpha parameter for pair potential between I and J (can - be computed from bulk modulus of reference structure + be computed from bulk modulus of reference structure) re(I,J) = equilibrium distance between I and J in the reference structure Cmax(I,J,K) = Cmax screening parameter when I-J pair is screened @@ -283,8 +283,8 @@ The recognized keywords for the parameter file are as follows: 1 = rho_bkgd = rho0_meam(a)\*Z_meam(a) (matches DYNAMO) default = 0 -Rc, delr, re are in distance units (Angstroms in the case of metal -units). Ec and delta are in energy units (eV in the case of metal +*Rc*, *delr*, *re* are in distance units (Angstroms in the case of metal +units). *Ec* and *delta* are in energy units (eV in the case of metal units). Each keyword represents a quantity which is either a scalar, vector, @@ -299,37 +299,37 @@ Thus these lines rho0(2) = 2.25 alpha(1,2) = 4.37 -set rho0 for the second element to the value 2.25 and set alpha for the +set *rho0* for the second element to the value 2.25 and set *alpha* for the alloy interaction between elements 1 and 2 to 4.37. -The augt1 parameter is related to modifications in the MEAM +The *augt1* parameter is related to modifications in the MEAM formulation of the partial electron density function. In recent literature, an extra term is included in the expression for the third-order density in order to make the densities orthogonal (see for example :ref:`(Wang) `, equation 3d); this term is included in the MEAM implementation in lammps. However, in earlier published work this term was not included when deriving parameters, including most of -those provided in the library.meam file included with lammps, and to -account for this difference the parameter t1 must be augmented by -3/5\*t3. If augt1=1, the default, this augmentation is done +those provided in the ``library.meam`` file included with lammps, and to +account for this difference the parameter *t1* must be augmented by +3/5\**t3*. If *augt1* = 1, the default, this augmentation is done automatically. When parameter values are fit using the modified density function, as in more recent literature, augt1 should be set to 0. -The mixture_ref_t parameter is available to match results with those +The *mixture_ref_t* parameter is available to match results with those of previous versions of lammps (before January 2011). Newer versions -of lammps, by default, use the single-element values of the t +of lammps, by default, use the single-element values of the *t* parameters to compute the background reference density. This is the proper way to compute these parameters. Earlier versions of lammps -used an alloy mixture averaged value of t to compute the background -reference density. Setting mixture_ref_t=1 gives the old behavior. -WARNING: using mixture_ref_t=1 will give results that are demonstrably +used an alloy mixture averaged value of *t* to compute the background +reference density. Setting *mixture_ref_t* = 1 gives the old behavior. +WARNING: using *mixture_ref_t* = 1 will give results that are demonstrably incorrect for second-neighbor MEAM, and non-standard for first-neighbor MEAM; this option is included only for matching with previous versions of lammps and should be avoided if possible. -The parameters attrac and repuls, along with the integer selection -parameter erose_form, can be used to modify the Rose energy function +The parameters *attrac* and *repuls*, along with the integer selection +parameter *erose_form*, can be used to modify the Rose energy function used to compute the pair potential. This function gives the energy of the reference state as a function of interatomic spacing. The form of this function is: @@ -343,19 +343,19 @@ this function is: a3 = repuls, astar < 0 a3 = attrac, astar >= 0 -Most published MEAM parameter sets use the default values attrac=repulse=0. -Setting repuls=attrac=delta corresponds to the form used in several +Most published MEAM parameter sets use the default values *attrac* = *repulse* = 0. +Setting *repuls* = *attrac* = *delta* corresponds to the form used in several recent published MEAM parameter sets, such as :ref:`(Valone) ` .. note:: - The default form of the erose expression in LAMMPS was corrected + The default form of the *erose* expression in LAMMPS was corrected in March 2009. The current version is correct, but may show different behavior compared with earlier versions of lammps with the attrac and/or repuls parameters are non-zero. To obtain the previous default - form, use erose_form = 1 (this form does not seem to appear in the + form, use *erose_form* = 1 (this form does not seem to appear in the literature). An alternative form (see e.g. :ref:`(Lee2) `) is - available using erose_form = 2. + available using *erose_form* = 2. ---------- @@ -364,13 +364,13 @@ Mixing, shift, table, tail correction, restart, rRESPA info For atom type pairs I,J and I != J, where types I and J correspond to two different element types, mixing is performed by LAMMPS with -user-specifiable parameters as described above. You never need to -specify a pair_coeff command with I != J arguments for this style. +user-specifiable parameters as described above. This pair style does not support the :doc:`pair_modify ` -shift, table, and tail options. +*shift*, *table*, and *tail* options. -This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you +This pair style does not write its information to :doc:`binary restart files `, +since it is stored in potential files. Thus, you need to re-specify the pair_style and pair_coeff commands in an input script that reads a restart file.