Second Moment Aproximation to the Tight Binding addes as pair style

doc/src/Commands_pair.rst

@@ -245,6 +245,8 @@ OPT.
    * :doc:`resquared (go) <pair_resquared>`
    * :doc:`saip/metal <pair_saip_metal>`
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
+   * :doc:`smatb <pair_smatb>`
+   * :doc:`smatb/single <pair_smatb>`
    * :doc:`smd/hertz <pair_smd_hertz>`
    * :doc:`smd/tlsph <pair_smd_tlsph>`
    * :doc:`smd/tri_surface <pair_smd_triangulated_surface>`

doc/src/Packages_details.rst

@@ -2578,18 +2578,20 @@ SMTBQ package
 
 **Contents:**
 
-A pair style which implements a Second Moment Tight Binding model with
-QEq charge equilibration (SMTBQ) potential for the description of
-ionocovalent bonds in oxides.
+Pair styles which implement Second Moment Tight Binding models.
+One with QEq charge equilibration (SMTBQ) for the description of
+ionocovalent bonds in oxides, and two more as plain SMATB models.
 
-**Authors:** Nicolas Salles, Emile Maras, Olivier Politano, and Robert
-Tetot (LAAS-CNRS, France).
+**Authors:** SMTBQ: Nicolas Salles, Emile Maras, Olivier Politano, and Robert
+Tetot (LAAS-CNRS, France);
+SMATB: Daniele Rapetti (Politecnico di Torino)
 
 **Supporting info:**
 
 * src/SMTBQ: filenames -> commands
 * src/SMTBQ/README
 * :doc:`pair_style smtbq <pair_smtbq>`
+* :doc:`pair_style smatb <pair_smatb>`, :doc:`pair_style smatb/single <pair_smatb>`
 * examples/PACKAGES/smtbq
 
 ----------

doc/src/Packages_list.rst

@@ -429,8 +429,8 @@ whether an extra library is needed to build and use the package:
      - n/a
      - no
    * - :ref:`SMTBQ <PKG-SMTBQ>`
-     - second moment tight binding potential
-     - :doc:`pair_style smtbq <pair_smtbq>`
+     - second moment tight binding potentials
+     - :doc:`pair_style smtbq <pair_smtbq>` :doc:`pair_style smatb <pair_smatb>`
      - PACKAGES/smtbq
      - no
    * - :ref:`SPH <PKG-SPH>`

doc/src/pair_smatb.rst

@@ -0,0 +1,131 @@
+.. index:: pair_style smatb
+.. index:: pair_style smatb/single
+
+pair_style smatb command
+=========================
+
+pair_style smatb/single command
+===============================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style style args
+
+* style = *smatb*
+* args = none
+
+.. parsed-literal::
+
+     *smatb*
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style smatb
+   pair_coeff 1 1 2.88 10.35 4.178 0.210 1.818 4.07293506 4.9883063257983666
+
+
+Description
+"""""""""""
+
+The *smatb* styles compute the Second Moment Approximation to the Tight Binding
+:ref:`(Cyrot) <Cyrot>`, :ref:`(Gupta) <Gupta>`, :ref:`(Rosato) <Rosato>`,
+given by
+
+.. math::
+      E_{i}  = \sum_{j,R_{ij}\leq R_{c}} \alpha(R_{ij}) - \sqrt{\sum_{j,R_{ij}\leq R_{c}}\Xi^2(R_{ij})}
+
+:math:`R_{ij}` is the distance between the atom :math:`i` and :math:`j`.
+And the two functions :math:`\alpha\left(r\right)` and :math:`\Xi\left(r\right)` are:
+
+.. math::
+   \alpha\left(r\right)=\left\lbrace\begin{array}{ll}
+      A e^{-p \left(\frac{r}{R_{0}}-1\right)} & r < R_{sc}\\
+      a_3\left(r-R_{c}\right)^3+a_4\left(r-R_{c}\right)^4
+      +a_5\left(r-R_{c}\right)^5& R_{sc} < r < R_{c}
+      \end{array}
+      \right.
+
+.. math::
+      \Xi\left(r\right)=\left\lbrace\begin{array}{ll}
+      \xi e^{-q \left(\frac{r}{R_{0}}-1\right)} & r < R_{sc}\\
+      x_3\left(r-R_{c}\right)^3+x_4\left(r-R_{c}\right)^4
+      +x_5\left(r-R_{c}\right)^5& R_{sc} < r < R_{c}
+      \end{array}
+      \right.
+
+
+The polynomial coefficients :math:`a_3`, :math:`a_4`, :math:`a_5`,
+:math:`x_3`, :math:`x_4`, :math:`x_5` are computed by LAMMPS: the two
+exponential terms and their first and second derivatives are smoothly
+reduced to zero, from the inner cutoff :math:`R_{sc}` to the outer
+cutoff :math:`R_{c}`.
+
+Coefficients
+""""""""""""
+
+The following coefficients must be defined for each pair of atoms types via the
+:doc:`pair_coeff <pair_coeff>` command as in the examples above, or in the data
+file or restart files read by the :doc:`read_data <read_data>` or
+:doc:`read_restart <read_restart>` commands, or by mixing as described below:
+
+* :math:`R_{0}` (distance units)
+* :math:`p` (dimensionless)
+* :math:`q` (dimensionless)
+* :math:`A` (energy units)
+* :math:`\xi` (energy units)
+* :math:`R_{cs}` (distance units)
+* :math:`R_{c}` (distance units)
+
+
+Note that: :math:`R_{0}` is the nearest neighbor distance, usually coincides
+with the diameter of the atoms
+
+See the :doc:`run_style <run_style>` command for details.
+
+----------
+
+Mixing info
+"""""""""""
+
+For atom type pairs I,J and I != J the coefficients are not automatically mixed.
+
+----------
+
+Restrictions
+""""""""""""
+
+This pair style is part of the SMTBQ package and is only enabled
+if LAMMPS is built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+
+These pair potentials require the :doc:`newton <newton>` setting to be "on" for pair interactions.
+
+Related commands
+""""""""""""""""
+
+* :doc:`pair_coeff <pair_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Cyrot:
+
+**(Cyrot)**  Cyrot-Lackmann and Ducastelle, Phys Rev. B, 4, 2406-2412 (1971).
+
+.. _Gupta:
+
+**(Gupta)** Gupta ,Phys Rev. B, 23, 6265-6270 (1981).
+
+.. _Rosato:
+
+**(Rosato)** Rosato and Guillope  and Legrand, Philosophical Magazine A, 59.2, 321-336 (1989).
+

doc/src/pair_style.rst

@@ -323,6 +323,8 @@ accelerated styles exist.
 * :doc:`resquared <pair_resquared>` - Everaers RE-Squared ellipsoidal potential
 * :doc:`saip/metal <pair_saip_metal>` - interlayer potential for hetero-junctions formed with hexagonal 2D materials and metal surfaces
 * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
+* :doc:`smatb <pair_smatb>` - Second Moment Approximation to the Tight Binding
+* :doc:`smatb/single <pair_smatb>` - Second Moment Approximation to the Tight Binding for single-element systems
 * :doc:`smd/hertz <pair_smd_hertz>` -
 * :doc:`smd/tlsph <pair_smd_tlsph>` -
 * :doc:`smd/tri_surface <pair_smd_triangulated_surface>` -

doc/utils/sphinx-config/false_positives.txt

@@ -693,6 +693,7 @@ DFT
 dftb
 dh
 dhex
+di
 dia
 diag
 diagonalization
@@ -784,6 +785,7 @@ dtheta
 dtshrink
 du
 dU
+Ducastelle
 Dudarev
 Duin
 Dullweber
@@ -1246,6 +1248,7 @@ Gubbins
 Guenole
 Guericke
 gui
+Guillope
 Gumbsch
 Gunsteren
 Gunzenmuller
@@ -1722,6 +1725,7 @@ lebedeva
 Lebedeva
 Lebold
 Lechman
+Legrand
 Lehoucq
 Leimkuhler
 Leite
@@ -2636,6 +2640,7 @@ Polarizable
 polarizables
 polarizer
 Politano
+Politecnico
 polyA
 polybond
 polydisperse
@@ -2794,6 +2799,7 @@ Randisi
 randomizations
 rann
 RANN
+Rapetti
 Raphson
 Rappe
 Ravelo
@@ -2939,6 +2945,7 @@ Rohart
 Ronchetti
 Ronevich
 Rosati
+Rosato
 Rosenberger
 Rossky
 rosybrown
@@ -3115,6 +3122,7 @@ smallbig
 smallint
 Smallint
 smallsmall
+smatb
 smd
 SMD
 smi
@@ -3383,6 +3391,7 @@ toolchain
 topologies
 Toporov
 Torder
+Torino
 torsions
 Tosi
 Toukmaji

examples/PACKAGES/smtbq/AgCuPancake.data

@@ -0,0 +1,48 @@
+# AgCu Pancake : energy should be around -90.16 eV
+34 atoms
+2 atom types
+0 30 xlo xhi
+0 30 ylo yhi
+0 30 zlo zhi
+
+Masses
+
+1  108 # Ag
+2  64  # Cu
+
+Atoms  # atomic
+
+1 1 11.8677744 17.4748811 16.8202155
+2 1 14.4591543 12.6388264 17.3769114
+3 1 19.2905996 14.8698601 15.9074284
+4 1 13.6418392 11.2583912 15.0376329
+5 1 16.5295136 18.8875825 16.3408808
+6 1 11.4394217 12.6680604 13.934792
+7 1 17.1772792 13.4579369 17.0971284
+8 1 11.7477198 12.5836832 16.6835448
+9 1 12.3254647 15.127665 12.9151285
+10 1 11.5595413 17.5592601 14.0713777
+11 1 18.9820568 14.9536515 13.1587506
+12 1 14.5653354 15.1189885 11.12255
+13 1 14.5797485 17.250847 17.5049696
+14 1 13.9305528 12.7833817 12.6633235
+15 1 12.8538576 14.9830633 17.6286053
+16 1 16.7229337 16.4525301 12.4627193
+17 1 14.0512024 17.3954338 12.7914031
+18 1 18.2824041 17.2316517 14.6999911
+19 1 16.2210303 18.9719703 13.5921161
+20 1 17.2517138 16.3080477 17.1761679
+21 1 16.0269821 11.057668 13.3712031
+22 1 16.3354169 10.9735982 16.1199203
+23 1 13.9149278 18.8223918 15.2392839
+24 1 18.1136886 12.5568867 14.5759053
+25 1 16.6484505 13.6019749 12.3834541
+26 1 11.0468778 15.1307677 15.4471491
+27 1 15.4347551 14.8811145 18.8773723
+28 2 15.1502129 14.9589199 16.3394186
+29 2 13.2837251 13.9076768 15.1588849
+30 2 13.4425035 16.3005712 15.2145264
+31 2 15.7534979 16.8960911 14.9738557
+32 2 15.4967806 13.024304 14.8837423
+33 2 14.8498337 15.0410649 13.6605697
+34 2 17.0232044 14.8712576 14.7690776

examples/PACKAGES/smtbq/in.smatbAgCuPancake

@@ -0,0 +1,38 @@
+# -*- lammps -*-
+
+units           metal
+atom_style      atomic
+boundary	p p p
+
+read_data	AgCuPancake.data
+
+pair_style	smatb
+#   	         NN     p	    q	    a  	    qsi	    cutOff_Start	cutOff_End
+pair_coeff	1 1 2.89	10.85	3.18	0.1031	1.1895	4.08707719	5.0056268338740553
+pair_coeff	1 2 2.725	10.70	2.805	0.0977	1.2275	4.08707719	4.4340500673763259
+pair_coeff	2 2 2.56	10.55	2.43	0.0894	1.2799	3.62038672	4.4340500673763259
+
+
+neighbor	8.0 bin
+neigh_modify	every 1 delay 0 check yes
+
+thermo          1
+minimize       1.0e-8 1.0e-10 10000 100000
+
+velocity            all create 600.0 761341 rot yes mom yes
+
+fix		1 all nve
+thermo		10
+timestep	0.005
+
+#dump		1 all atom 50 dump.smatb
+
+#dump		2 all image 10 image.*.jpg element element &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	2 pad 3 element Ag Cu
+
+#dump		3 all movie 10 movie.mpg element element &
+#		axes yes 0.8 0.02 view 60 -30
+#dump_modify	3 pad 3 element Ag Cu
+
+run		10000

examples/PACKAGES/smtbq/in.smatbBulkFCC

@@ -0,0 +1,27 @@
+# -*- lammps -*-
+
+units           metal
+atom_style      atomic
+boundary	p p p
+
+lattice fcc 4.0782
+
+region myreg block 0 8 0 8 0 8
+
+create_box      1 myreg
+
+create_atoms    1 box
+
+mass 1 196.96655  # Au
+
+pair_style	smatb/single
+pair_coeff	1 1 2.88 10.35	4.178	0.210	1.818	4.07293506	4.9883063257983666
+
+neighbor	8.0 bin
+neigh_modify	every 1 delay 0 check yes
+
+thermo          1
+fix            boxmin all box/relax iso 1.0
+minimize       1.0e-8 1.0e-10 10000 100000
+unfix boxmin
+minimize       1.0e-8 1.0e-10 10000 100000