All posts




 
karls
Upcoming additions to EDIP_BOP_C__MD_506186535567_000
Currently planned future additions to this Model Driver (MD) include: 1.) Support for the NEIGH_RVEC_F NBC method 2.) Support for multiple species. This will allow the MD to perform simulations on systems consisting of Si, C, or SiC After item 2 is implemented, I plan to create a Model based on the following article (pending permission of its authors, of course): G. Lucas, M. Bertolus, and L. Pizzagalli, "An environment-dependent interatomic potential for silicon carbide: calculation of bulk properties, high-pressure phases, point and extended defects, and amorphous structures," J. Phys.: Condens. Matter, vol. 22, pp. 035802, 2010.
31-Mar-2014 01:19PM CDT

 
Ryan
Conversion of LAMMPS 2NN MEAM parameters to 2NN MEAM potential parametes for MEAM_2NN__MD_111291751625_000
The following information was provided by Prof. Byeong-Joo Lee of POSTECH (Pohang University of Science and Technology) on 31-Mar-2014. In the below, the "current KIM code" refers to the Model Driver MEAM_2NN__MD_111291751625_000. Parameters surrounded by **'s deserve special attention, as they are associated with incompatibilities between LAMMPS and MEAM_2NN__MD_111291751625_000. ---------- LAMMPS to KIM conversion of 2NN MEAM potential parameters. 1. library.meam 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** # CAUTION: In the current KIM code, only t0=1 is available. # CAUTION: The ibar parameter selects the form of the function G(Gamma) used to compute the electron density; options are 0: G = sqrt(q+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)). In the current KIM code, only option 3 is available. 2. MEAM parameter file 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 The recognized keywords are as follows: rc = cutoff radius for cutoff function; default = 4.0 **delr** = length of smoothing distance for cutoff function; default = 0.1 # CAUTION: In the current KIM code, only default value is available. 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) # CAUTION: In the current KIM code, ‘c11’ is not supported. **nn2(I,J)** = turn on second-nearest neighbor MEAM formulation for I-J pair. 0 = second-nearest neighbor formulation off 1 = second-nearest neighbor formulation on default = 0 # CAUTION: In the current KIM code, only option 1 is available. **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 # CAUTION: In the current KIM code, attrac and repuls should be same value. **zbl(I,J)** = blend the MEAM I-J pair potential with the ZBL potential for small atom separations (ZBL); default = 1 # CAUTION: In the current KIM code, only zero value is available. **gsmooth_factor** = factor determining the length of the G-function smoothing region; only significant for ibar=0 or ibar=4. # CAUTION: In the current KIM code, only ibar=3 option is available, therefore this value is negligible. **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 # CAUTION: In the current KIM code, only option 0 is available. **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 # CAUTION: In the current KIM code, only option 2 is available. **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 0 = do not use mixture averaging for t in the reference density 1 = use mixture averaging for t in the reference density default = 0 # CAUTION: In the current KIM code, only default option is available. **erose_form** = integer value to select the form of the Rose energy function 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 default = 0 # CAUTION: In the current KIM code, only option 2 is available. **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 # CAUTION: In the current KIM code, only default option is available. **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 # CAUTION: In the current KIM code, only default option is available. 3. Conversion to the KIM The MEAM parameters mentioned above should be written in eam_db.tdb file. The file name should not be changed. The values in eam_db.tdb file should be represented in fixed format, which means that the values should be put in place. See the example in the following. eam_tb.tdb: 1 10 20 30 40 50 60 70 80 1 El Ref.St mass Ec Re B A beta(0) beta(1) 2 beta(2) beta(3) t(1) t(2) t(3) Rho_zero Cmin 3 Fe BCC_A2 55.847d+00 4.28d+00 2.469d+00 1.0372d+00 0.585d+0 3.80d+00 2.00d+00 4 0.30 3.60 0.90d+00 0.00d+00 -0.80d+00 12.30d+00 2.00d+00 1.00d+00 0.681.90 5 C DIA_A4 12.011d+00 7.37d+00 1.545d+00 2.7692d+00 1.49d+00 4.26d+00 5.00d+00 6 0.00 4.00 3.20d+00 3.98d+00 7.50d+00 1.04d+00 -1.01d+00 5.49d+00 2.002.80 7 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 8 Alloy Ref.St delta_Ec Re B Eu_d Ciji Cjij Ciij Cijj AU 9 Fe-C FCC_B1 0.0023d+00 1.9200d+00 2.0632d+00 0.13 0.06 0.51 2.00 2.00 BJ 10 4.50 2.80 2.80 2.80 2.80 EOF 3-1. Parameters for pure element El [1st line, 01:02] = elt in library file. dimensionless. Ref.St [1st line, 04:09] = lattice(i,i) in MEAM parameter file. dimensionless. fcc -> FCC_A1 bcc -> BCC_A2 hcp -> HCP_A3 dia -> DIA_A4 dim -> DIMER mass [1st line, 10:21] = atwt in library file (g/mol). Ec [1st line, 22:30] = esub in library file or Ec(i,i) in MEAM parameter file (eV/atom). Re [1st line, 31:40] = computed from alat in library file or re(i,i) in MEAM parameter file (Å). B [1st line, 41:51] = computed from alpha in library file or alpha(i,i) in MEAM parameter file (eV/Å3). B = (alpha*alpha*Ec)/(9*omega) where omega is atomic volume of the reference structure. A [1st line, 52:60] = asub in library file. dimensionless. beta(1-2)[1st line, 61:69, 70:78] = b1, b2 in library file. dimensionless. d [2nd line, 04:07] = repuls(i,i)(=attrac(i,i)) in MEAM parameter file. dimensionless. Rcut [2nd line, 08:12] = rc in MEAM parameter file (Å). The maximum values among Rcut of each element or pair would be set for cutoff distance. beta(3-4) [2nd line, 13:21, 22:30] = b3, b4 in library file. dimensionless. t(1-3) [2nd line, 31:40, 41:50, 51-60] = t1, t2, t3 in library file. dimensionless. Rho_zero [2nd line, 61:69] = rozero in library file or rho0(i) in MEAM parameter file. dimensionless. Cmin [2nd line, 70:74] = Cmin(i,i,i) in MEAM parameter file. dimensionless. Cmax [2nd line, 75:78] = Cmax(i,i,i) in MEAM parameter file. dimensionless. 3-2. Parameters for binary system pair [1nd line, 01:05] Ref.St [1st line, 08:13] = lattice(i,j) in MEAM parameter file. dimensionless. b1 -> FCC_B1 b2 -> BCC_B2 b3 -> ZnS_B3 l12 -> L12AB3 or L12A3B delta_Ec [1st line, 14:25] = delta(i,j) in MEAM parameter file (eV/atom). Re [1st line, 26:37] = re(i,j) in MEAM parameter file (Å). B [1st line, 38:49] = computed from alpha(i,j) in MEAM parameter file (eV/Å3). B = (alpha*alpha*Ec)/(9*omega) where omega is atomic volume of the reference structure. Eu_d [1st line, 51:55] = repuls(i,j)(=attrac(i,j)) in MEAM parameter file. dimensionless. **Cmin(i,j,k)** [1st line, 56:60, 61:65, 66:70, 71:75] = Cmin(i,k,j) in MEAM parameter file. dimensionless. # CAUTION: The sequence of i, j, k is different in KIM and LAMMPS. In the current KIM code, Cmin(i,j,k) means when i-k pair is screeened by j while in L!AMMPS, when i-j pair is screened by k. Rcut [2nd line, 51:55] = rc in MEAM parameter file (Å). The maximum values among Rcut of each element or pair would be set for cutoff distance. **Cmax(i,j,k)** [2nd line, 56:60, 61:65, 66:70, 71:75] = Cmax(i,k,j) in MEAM parameter file. dimensionless. # CAUTION: The sequence of i, j, k is different in KIM and LAMMPS. In the current KIM code, Cmin(i,j,k) means when i-k pair is screeened by j while in LAMMPS, when i-j pair is screened by k.
02-Apr-2014 12:00PM CDT

 
karls
Comparison to literature for EDIP calculation of monovacancy formation energy in Silicon
The Test Result of the #EDIP_BOP_Bazant_Kaxiras_Si__MO_958932894036_000 Model when paired against the #RelaxedMonovacancy_diamond_Si__TE_918374098712_000 Test looks to be in perfect agreement with literature. In one of the original publications of the EDIP potential for Silicon--[ J.F. Justo, M.Z. Bazant, E. Kaxiras, V.V. Bulatov, and S. Yip. "Interatomic potential for silicon defects and disordered phases," Phys. Rev. B, 58, 2539-2550, 1998. Available at http://journals.aps.org/prb/abstract/10.1103/PhysRevB.58.2539]---the authors report the unrelaxed formation energy of a monovacancy in diamond Silicon to be 3.46eV (see Table IV of the article). They also report that the energy difference between the unrelaxed and relaxed configurations is 0.25eV. Looking at the corresponding results in the KIM pipeline, i.e. results.yaml of #TE_918374098712_000-and-MO_958932894036_000, we see the unrelaxed formation energy of the monovacancy is computed to be 3.46467eV and the relaxed formation energy is computed to be 3.21848eV. The difference between these two quantities is 0.24619eV, which closely matches the above result given in the literature.
30-Mar-2014 01:43PM CDT

 
karls
Consult LAMMPS tutorial for more info on these Tests
I encourage anyone looking at the following Tests: - #LammpsExample__TE_565333229701_000 - #LammpsExample2_diamond_Si__TE_837477125670_000 - #LammpsExample2_fcc_Ar__TE_778998786610_000 to consult the tutorial for creating KIM-compliant LAMMPS Tests (available at https://pipeline.openkim.org/docs/tutorial_lammps.html or by selecting "Pipeline" at the top of the page, then "Documentation" and clicking on "Example tests - LAMMPS" under the FAQs section). This tutorial explains the general format and structure of the Tests, as well as how KIM and LAMMPS interact with one another. You may also want to take at look at the tutorial for creating KIM-compliant ASE Tests. This can be found at https://pipeline.openkim.org/docs/tutorial_ase.html or by clicking on "Example test - ASE" in the FAQs section of the OpenKIM Pipeline documentation page.
30-Mar-2014 02:42PM CDT