diff --git a/doc/txt/pair_meamc.txt b/doc/txt/pair_meamc.txt deleted file mode 100644 index 2831600e08..0000000000 --- a/doc/txt/pair_meamc.txt +++ /dev/null @@ -1,402 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Commands_all.html) - -:line - -pair_style meam/c command :h3 - -[Syntax:] - -pair_style style :pre - -style = {meam/c} - -[Examples:] - -pair_style meam/c -pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si -pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre - -[Description:] - -NOTE: The behavior of the MEAM potential for alloy systems has changed -as of November 2010; see description below of the mixture_ref_t -parameter - -Style {meam/c} computes pairwise interactions for a variety of materials -using modified embedded-atom method (MEAM) potentials -"(Baskes)"_#Baskes. Conceptually, it is an extension to the original -"EAM potentials"_pair_eam.html which adds angular forces. It is -thus suitable for modeling metals and alloys with fcc, bcc, hcp and -diamond cubic structures, as well as covalently bonded materials like -silicon and carbon. Style {meam/c} is a translation of the (now obsolete) -{meam} code from Fortran to C++. It is functionally equivalent to {meam} -but more efficient, and thus {meam} has been removed from LAMMPS after -the 12 December 2018 release. - -In the MEAM formulation, the total energy E of a system of atoms is -given by: - -:c,image(Eqs/pair_meam.jpg) - -where F is the embedding energy which is a function of the atomic -electron density rho, and phi is a pair potential interaction. The -pair interaction is summed over all neighbors J of atom I within the -cutoff distance. As with EAM, the multi-body nature of the MEAM -potential is a result of the embedding energy term. Details of the -computation of the embedding and pair energies, as implemented in -LAMMPS, are given in "(Gullet)"_#Gullet and references therein. - -The various parameters in the MEAM formulas are listed in two files -which are specified by the "pair_coeff"_pair_coeff.html command. -These are ASCII text files in a format consistent with other MD codes -that implement MEAM potentials, such as the serial DYNAMO code and -Warp. Several MEAM potential files with parameters for different -materials are included in the "potentials" directory of the LAMMPS -distribution with a ".meam" suffix. All of these are parameterized in -terms of LAMMPS "metal units"_units.html. - -Note that unlike for other potentials, cutoffs for MEAM potentials are -not set in the pair_style or pair_coeff command; they are specified in -the MEAM potential files themselves. - -Only a single pair_coeff command is used with the {meam} style which -specifies two MEAM files and the element(s) to extract information -for. The MEAM elements are mapped to LAMMPS atom types by specifying -N additional arguments after the 2nd filename in the pair_coeff -command, where N is the number of LAMMPS atom types: - -MEAM library file -Elem1, Elem2, ... -MEAM parameter file -N element names = mapping of MEAM elements to atom types :ul - -See the "pair_coeff"_pair_coeff.html doc 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 -LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si, -and the 4th to be C, you would use the following pair_coeff command: - -pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre - -The 1st 2 arguments must be * * so as to span all LAMMPS atom types. -The two filenames are for the library and parameter file respectively. -The Si and C arguments (between the file names) are the two elements -for which info will be extracted from the library file. The first -three trailing Si arguments map LAMMPS atom types 1,2,3 to the MEAM Si -element. The final C argument maps LAMMPS atom type 4 to the MEAM C -element. - -If the 2nd filename is specified as NULL, no parameter file is read, -which simply means the generic parameters in the library file are -used. Use of the NULL specification for the parameter file is -discouraged for systems with more than a single element type -(e.g. alloys), since the parameter file is expected to set element -interaction terms that are not captured by the information in the -library file. - -If a mapping value is specified as NULL, the mapping is not performed. -This can be used when a {meam} potential is used as part of the -{hybrid} pair style. The NULL values are placeholders for atom types -that will be used with other potentials. - -NOTE: If the 2nd 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 2nd filename is not NULL (as in the -example above), it contains settings that are Fortran-indexed for the -elements that preceed it. Thus you need to insure you list the -elements between the filenames in an order consistent with how the -values in the 2nd filename are indexed. See details below on the -syntax for settings in the 2nd 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 -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 -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 -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 1st matching entry it -finds and ignores the rest. - -Other parameters in the MEAM library file correspond to single-element -potential parameters: - -lat = lattice structure of reference configuration -z = number of nearest neighbors in the reference structure - This field is only read for compatibility, the correct - value is inferred from the lattice structure -ielement = atomic number -atwt = atomic weight -alat = lattice constant of reference structure -esub = energy per atom (eV) in the reference structure at equilibrium -asub = "A" parameter for MEAM (see e.g. "(Baskes)"_#Baskes) :pre - -The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the -standard MEAM parameters in the literature "(Baskes)"_#Baskes (the b -parameters are the standard beta parameters). Note that only parameters -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 "(Gullet)"_#Gullet) and -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 - - 0 => G = sqrt(1+Gamma) - 1 => G = exp(Gamma/2) - 2 => not implemented - 3 => G = 2/(1+exp(-Gamma)) - 4 => G = sqrt(1+Gamma) - -5 => G = +-sqrt(abs(1+Gamma)) :pre - -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 -line has one of the following forms. Each line can also have a -trailing comment (starting with #) which is ignored. - -keyword = value -keyword(I) = value -keyword(I,J) = value -keyword(I,J,K) = value :pre - -The indices I, J, K correspond to the elements selected from the -MEAM library file numbered in the order of how those elements were -selected starting from 1. Thus for the example given below - -pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre - -an index of 1 would refer to Si and an index of 2 to C. - -The recognized keywords for the parameter file are as follows: - -Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr, -augt1, gsmooth_factor, re - -where - -rc = cutoff radius for cutoff function; default = 4.0 -delr = length of smoothing distance for cutoff function; default = 0.1 -rho0(I) = relative density for element I (overwrites value - read from meamf file) -Ec(I,J) = cohesive energy of reference structure for I-J mixture -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 -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 - by K (I<=J); default = 2.8 -Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened - by K (I<=J); default = 2.0 -lattce(I,J) = lattice structure of I-J reference structure: - dia = diamond (interlaced fcc for alloy) - fcc = face centered cubic - bcc = body centered cubic - dim = dimer - b1 = rock salt (NaCl structure) - hcp = hexagonal close-packed - c11 = MoSi2 structure - l12 = Cu3Au structure (lower case L, followed by 12) - b2 = CsCl structure (interpenetrating simple cubic) -nn2(I,J) = turn on second-nearest neighbor MEAM formulation for - I-J pair (see for example "(Lee)"_#Lee). - 0 = second-nearest neighbor formulation off - 1 = second-nearest neighbor formulation on - default = 0 -attrac(I,J) = additional cubic attraction term in Rose energy I-J pair potential - default = 0 -repuls(I,J) = additional cubic repulsive term in Rose energy I-J pair potential - default = 0 -zbl(I,J) = blend the MEAM I-J pair potential with the ZBL potential for small - atom separations "(ZBL)"_#ZBL - default = 1 -gsmooth_factor = factor determining the length of the G-function smoothing - region; only significant for ibar=0 or ibar=4. - 99.0 = short smoothing region, sharp step - 0.5 = long smoothing region, smooth step - default = 99.0 -augt1 = integer flag for whether to augment t1 parameter by - 3/5*t3 to account for old vs. new meam formulations; - 0 = don't augment t1 - 1 = augment t1 - default = 1 -ialloy = integer flag to use alternative averaging rule for t parameters, - for comparison with the DYNAMO MEAM code - 0 = standard averaging (matches ialloy=0 in DYNAMO) - 1 = alternative averaging (matches ialloy=1 in DYNAMO) - 2 = no averaging of t (use single-element values) - default = 0 -mixture_ref_t = integer flag to use mixture average of t to compute the background - reference density for alloys, instead of the single-element values - (see description and warning elsewhere in this doc page) - 0 = do not use mixture averaging for t in the reference density - 1 = use mixture averaging for t in the reference density - default = 0 -erose_form = integer value to select the form of the Rose energy function - (see description below). - default = 0 -emb_lin_neg = integer value to select embedding function for negative densities - 0 = F(rho)=0 - 1 = F(rho) = -asub*esub*rho (linear in rho, matches DYNAMO) - default = 0 -bkgd_dyn = integer value to select background density formula - 0 = rho_bkgd = rho_ref_meam(a) (as in the reference structure) - 1 = rho_bkgd = rho0_meam(a)*Z_meam(a) (matches DYNAMO) - default = 0 :pre - -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, -2d array, or 3d array and must be specified with the correct -corresponding array syntax. The indices I,J,K each run from 1 to N -where N is the number of MEAM elements being used. - -Thus these lines - -rho0(2) = 2.25 -alpha(1,2) = 4.37 :pre - -set rho0 for the 2nd 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 -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 "(Wang)"_#Wang2, 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 -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 -of previous versions of lammps (before January 2011). Newer versions -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 -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 -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: - -astar = alpha * (r/re - 1.d0) -if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar) -if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar) -if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar) -a3 = repuls, astar < 0 -a3 = attrac, astar >= 0 :pre - -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 "(Valone)"_#Valone - -NOTE: 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 -literature). An alternative form (see e.g. "(Lee2)"_#Lee2) is -available using erose_form = 2. - -:line - -[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. - -This pair style does not support the "pair_modify"_pair_modify.html -shift, table, and tail options. - -This pair style does not write its information to "binary restart -files"_restart.html, 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. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -The {meam/c} style is provided in the USER-MEAMC package. It is -only enabled if LAMMPS was built with that package. -See the "Build package"_Build_package.html doc page for more info. - -The maximum number of elements, that can be read from the MEAM -library file, is determined at compile time. The default is 5. -If you need support for more elements, you have to change the -define for the constant 'maxelt' at the beginning of the file -src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no -limit on the number of atoms types. - -[Related commands:] - -"pair_coeff"_pair_coeff.html, "pair_style eam"_pair_eam.html, -"pair_style meam/spline"_pair_meam_spline.html - -[Default:] none - -:line - -:link(Baskes) -[(Baskes)] Baskes, Phys Rev B, 46, 2727-2742 (1992). - -:link(Gullet) -[(Gullet)] Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). -This report may be accessed on-line via "this link"_sandreport. - -:link(sandreport,http://infoserve.sandia.gov/sand_doc/2003/038782.pdf) - -:link(Lee) -[(Lee)] Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000). - -:link(Lee2) -[(Lee2)] Lee, Baskes, Kim, Cho. Phys. Rev. B, 64, 184102 (2001). - -:link(Valone) -[(Valone)] Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006). - -:link(Wang2) -[(Wang)] Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004). - -:link(ZBL) -[(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges -of Ions in Matter", Vol 1, 1985, Pergamon Press.