diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index 2c7723ab5dd19f9816968c9a4d28145ed1d67092..de184b347bad5e56b587c89c3c11e74adbd51d16 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -178,7 +178,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
- USER-QUIP USER-QMMM)
+ USER-QUIP USER-QMMM USER-YAFF)
set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
set(OTHER_PACKAGES CORESHELL QEQ)
foreach(PKG ${DEFAULT_PACKAGES})
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
index fbf292aab2798dbeeb5623f3f43dc8a169e3f367..3b79612e766c5649b93b8138e889c37bb5afb73e 100644
--- a/doc/src/Commands_bond.txt
+++ b/doc/src/Commands_bond.txt
@@ -37,6 +37,7 @@ OPT.
"harmonic (iko)"_bond_harmonic.html,
"harmonic/shift (o)"_bond_harmonic_shift.html,
"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
+"mm3"_bond_mm3.html,
"morse (o)"_bond_morse.html,
"nonlinear (o)"_bond_nonlinear.html,
"oxdna/fene"_bond_oxdna.html,
@@ -67,10 +68,12 @@ OPT.
"cosine/shift (o)"_angle_cosine_shift.html,
"cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
"cosine/squared (o)"_angle_cosine_squared.html,
+"cross"_angle_cross.html,
"dipole (o)"_angle_dipole.html,
"fourier (o)"_angle_fourier.html,
"fourier/simple (o)"_angle_fourier_simple.html,
"harmonic (iko)"_angle_harmonic.html,
+"mm3"_angle_mm3.html,
"quartic (o)"_angle_quartic.html,
"sdk (o)"_angle_sdk.html,
"table (o)"_angle_table.html :tb(c=4,ea=c)
@@ -120,8 +123,10 @@ OPT.
"cossq (o)"_improper_cossq.html,
"cvff (io)"_improper_cvff.html,
"distance"_improper_distance.html,
+"distharm"_improper_distharm.html,
"fourier (o)"_improper_fourier.html,
"harmonic (iko)"_improper_harmonic.html,
"inversion/harmonic"_improper_inversion_harmonic.html,
"ring (o)"_improper_ring.html,
+"sqdistharm"_improper_sqdistharm.html,
"umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
index 46f4950ad78fb60db7555b50810b318a56cd4147..b498e6bfdadc348034e849839c505d866af1639c 100644
--- a/doc/src/Commands_pair.txt
+++ b/doc/src/Commands_pair.txt
@@ -154,6 +154,7 @@ OPT.
"lj/sf/dipole/sf (go)"_pair_dipole.html,
"lj/smooth (o)"_pair_lj_smooth.html,
"lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
+"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
"lj96/cut (go)"_pair_lj96.html,
"lubricate (o)"_pair_lubricate.html,
"lubricate/poly (o)"_pair_lubricate.html,
diff --git a/doc/src/Eqs/angle_cross.jpg b/doc/src/Eqs/angle_cross.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..b0f3fcf83ac2621807c7ae58772bfbddd1d94824
Binary files /dev/null and b/doc/src/Eqs/angle_cross.jpg differ
diff --git a/doc/src/Eqs/angle_cross.tex b/doc/src/Eqs/angle_cross.tex
new file mode 100644
index 0000000000000000000000000000000000000000..9d1fdcb7f8e53e19e61b596e0e313d3050a46c4a
--- /dev/null
+++ b/doc/src/Eqs/angle_cross.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+ E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
+$$
+
+\end{document}
diff --git a/doc/src/Eqs/angle_mm3.jpg b/doc/src/Eqs/angle_mm3.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..5b9f3e34f091f5a2d439294e9c5a1802a2885fb4
Binary files /dev/null and b/doc/src/Eqs/angle_mm3.jpg differ
diff --git a/doc/src/Eqs/angle_mm3.tex b/doc/src/Eqs/angle_mm3.tex
new file mode 100644
index 0000000000000000000000000000000000000000..e2d96f2d6939db2c6eb3e0ad3cbdf6dd4e4c9321
--- /dev/null
+++ b/doc/src/Eqs/angle_mm3.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+ E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
+$$
+
+\end{document}
diff --git a/doc/src/Eqs/bond_mm3.jpg b/doc/src/Eqs/bond_mm3.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..2c17739db57e8d147166ab0a4cc768cf80f534af
Binary files /dev/null and b/doc/src/Eqs/bond_mm3.jpg differ
diff --git a/doc/src/Eqs/bond_mm3.tex b/doc/src/Eqs/bond_mm3.tex
new file mode 100644
index 0000000000000000000000000000000000000000..549500ebacc714b7106a864d4ba0b3d0d3f6bf7e
--- /dev/null
+++ b/doc/src/Eqs/bond_mm3.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+ E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
+$$
+
+\end{document}
diff --git a/doc/src/Eqs/improper_distharm.jpg b/doc/src/Eqs/improper_distharm.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..e55036b5bf092c1b35b8ba42427b78f562238947
Binary files /dev/null and b/doc/src/Eqs/improper_distharm.jpg differ
diff --git a/doc/src/Eqs/improper_distharm.tex b/doc/src/Eqs/improper_distharm.tex
new file mode 100644
index 0000000000000000000000000000000000000000..218de6a0ddc40ecd9021dd430647bc678c6e3fa0
--- /dev/null
+++ b/doc/src/Eqs/improper_distharm.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+ E = K (d - d_0)^2
+$$
+
+\end{document}
diff --git a/doc/src/Eqs/improper_sqdistharm.jpg b/doc/src/Eqs/improper_sqdistharm.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..b1a84e995e655ca32d6529122fa971bc1ef1e574
Binary files /dev/null and b/doc/src/Eqs/improper_sqdistharm.jpg differ
diff --git a/doc/src/Eqs/improper_sqdistharm.tex b/doc/src/Eqs/improper_sqdistharm.tex
new file mode 100644
index 0000000000000000000000000000000000000000..1b50a309a046a0b4fe4a32ce6b728f5666dfda10
--- /dev/null
+++ b/doc/src/Eqs/improper_sqdistharm.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+ E = K (d^2 - d_0^2)^2
+$$
+
+\end{document}
diff --git a/doc/src/Eqs/pair_coulgauss.jpg b/doc/src/Eqs/pair_coulgauss.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..bf84d90c4a1b4a7774e3933bfef6e949c9603cf7
Binary files /dev/null and b/doc/src/Eqs/pair_coulgauss.jpg differ
diff --git a/doc/src/Eqs/pair_coulgauss.tex b/doc/src/Eqs/pair_coulgauss.tex
new file mode 100644
index 0000000000000000000000000000000000000000..216d3b3360a791efb8ac8f29fe9dc887e87a97b5
--- /dev/null
+++ b/doc/src/Eqs/pair_coulgauss.tex
@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+ \thispagestyle{empty}
+\begin{eqnarray*}
+ E &=& \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/src/Eqs/pair_lj_switch3.jpg b/doc/src/Eqs/pair_lj_switch3.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..a1f98ea2c24bcac86871e1476901791edc83dc62
Binary files /dev/null and b/doc/src/Eqs/pair_lj_switch3.jpg differ
diff --git a/doc/src/Eqs/pair_lj_switch3.tex b/doc/src/Eqs/pair_lj_switch3.tex
new file mode 100644
index 0000000000000000000000000000000000000000..29161fb2ef679f9d2186dcf31335b5daacc5540b
--- /dev/null
+++ b/doc/src/Eqs/pair_lj_switch3.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+ \thispagestyle{empty}
+
+\begin{eqnarray*}
+ E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right]
+% \qquad r < r_c \\
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/src/Eqs/pair_mm3_switch3.jpg b/doc/src/Eqs/pair_mm3_switch3.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..5d662584a7d1fec8d273c87ce3bf0b16a904f6d4
Binary files /dev/null and b/doc/src/Eqs/pair_mm3_switch3.jpg differ
diff --git a/doc/src/Eqs/pair_mm3_switch3.tex b/doc/src/Eqs/pair_mm3_switch3.tex
new file mode 100644
index 0000000000000000000000000000000000000000..a80278cce2236c6f7ba4951cadb8fe781abc60d2
--- /dev/null
+++ b/doc/src/Eqs/pair_mm3_switch3.tex
@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+ \thispagestyle{empty}
+\begin{eqnarray*}
+ E &=& \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
+ r_{v,ij} &=& r_{v,i} + r_{v,j} \\
+ \epsilon_{ij} &=& \sqrt{\epsilon_i \epsilon_j}
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/src/Eqs/pair_switch3.jpg b/doc/src/Eqs/pair_switch3.jpg
new file mode 100644
index 0000000000000000000000000000000000000000..e6327ee5ff1d2b6e586e4d0fdfc879a4b9977a56
Binary files /dev/null and b/doc/src/Eqs/pair_switch3.jpg differ
diff --git a/doc/src/Eqs/pair_switch3.tex b/doc/src/Eqs/pair_switch3.tex
new file mode 100644
index 0000000000000000000000000000000000000000..7ae67a5e6548ed1b342a596ec3fbfbbec023891c
--- /dev/null
+++ b/doc/src/Eqs/pair_switch3.tex
@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+
+\begin{eqnarray*}
+ S_3(r) = \left\lbrace \begin{array}{ll}
+ 1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
+ 3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
+ 0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
+ \end{array} \right.
+\end{eqnarray*}
+
+\end{document}
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index 4768c50ca47d8ad2d9f8ec0634e4bf43f5ac2031..ebfe01d8a73a2cfbda9057cd761131313b3d0041 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -100,7 +100,8 @@ as contained in the file name.
"USER-SPH"_#PKG-USER-SPH,
"USER-TALLY"_#PKG-USER-TALLY,
"USER-UEF"_#PKG-USER-UEF,
-"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c)
+"USER-VTK"_#PKG-USER-VTK,
+"USER-YAFF"_#PKG-USER-YAFF, :tb(c=6,ea=c)
:line
@@ -2067,3 +2068,39 @@ lib/vtk/README
"dump vtk"_dump_vtk.html :ul
+:line
+
+USER-YAFF package :link(PKG-USER-YAFF),h4
+
+[Contents:]
+
+Some potentials that are also implemented in the Yet Another Force Field ("YAFF"_yaff) code.
+The expressions and their use are discussed in the following papers
+
+Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) "link"_vanduyfhuys2015
+Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) "link"_vanduyfhuys2018 :ul
+
+which discuss the "QuickFF"_quickff methodology.
+
+
+:link(vanduyfhuys2015,http://dx.doi.org/10.1002/jcc.23877)
+:link(vanduyfhuys2018,http://dx.doi.org/10.1002/jcc.25173)
+:link(quickff,http://molmod.github.io/QuickFF)
+:link(yaff,https://github.com/molmod/yaff)
+
+
+[Author:] Steven Vandenbrande.
+
+[Supporting info:]
+
+src/USER-YAFF/README
+"angle_style cross"_angle_cross.html
+"angle_style mm3"_angle_mm3.html
+"bond_style mm3"_bond_mm3.html
+"improper_style distharm"_improper_distharm.html
+"improper_style sqdistharm"_improper_sqdistharm.html
+"pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html
+"pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html
+examples/USER/yaff :ul
+
+
diff --git a/doc/src/Packages_user.txt b/doc/src/Packages_user.txt
index cea3db4377411c05272bae170c09625678e46cf0..4a702e971fe526c00298996da98776d2f0224f28 100644
--- a/doc/src/Packages_user.txt
+++ b/doc/src/Packages_user.txt
@@ -75,7 +75,8 @@ Package, Description, Doc page, Example, Library
"USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
"USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
"USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
-"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)
+"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext
+"USER-YAFF"_Packages_details.html#PKG-USER-YAFF, additional styles implemented in YAFF, "angle_style cross"_angle_cross.html, USER/yaff, no :tb(ea=c,ca1=l)
:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
:link(PLUMED,http://www.plumed.org)
diff --git a/doc/src/angle_cross.txt b/doc/src/angle_cross.txt
new file mode 100644
index 0000000000000000000000000000000000000000..d9d83ed4b69eef64c269f264382c1073259c0f5f
--- /dev/null
+++ b/doc/src/angle_cross.txt
@@ -0,0 +1,62 @@
+"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
+
+angle_style cross command :h3
+
+[Syntax:]
+
+angle_style cross :pre
+
+[Examples:]
+
+angle_style cross
+angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0 :pre
+
+[Description:]
+
+The {cross} angle style uses a potential that couples the bond stretches of
+a bend with the angle stretch of that bend:
+
+:c,image(Eqs/angle_cross.jpg)
+
+where r12,0 is the rest value of the bond length between atom 1 and 2,
+r32,0 is the rest value of the bond length between atom 2 and 2,
+and theta0 is the rest value of the angle. KSS is the force constant of
+the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants
+of the bond stretch-angle stretch terms.
+
+The following coefficients must be defined for each angle type via the
+"angle_coeff"_angle_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+KSS (energy/distance^2)
+KBS0 (energy/distance/rad)
+KBS1 (energy/distance/rad)
+r12,0 (distance)
+r32,0 (distance)
+theta0 (degrees) :ul
+
+Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of KBS0 and KBS1 are in energy/distance/radian.
+
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+USER_YAFF package. See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"angle_coeff"_angle_coeff.html
+
+[Default:] none
+
+:line
+
+
diff --git a/doc/src/angle_mm3.txt b/doc/src/angle_mm3.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9ae032c4ff5344f78267b50c1d4f81914c15d6f6
--- /dev/null
+++ b/doc/src/angle_mm3.txt
@@ -0,0 +1,55 @@
+"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
+
+angle_style mm3 command :h3
+
+[Syntax:]
+
+angle_style mm3 :pre
+
+[Examples:]
+
+angle_style mm3
+angle_coeff 1 100.0 107.0 :pre
+
+[Description:]
+
+The {mm3} angle style uses the potential that is anharmonic in the angle
+as defined in "(Allinger)"_#mm3-allinger1989
+
+:c,image(Eqs/angle_mm3.jpg)
+
+where theta0 is the equilibrium value of the angle, and K is a
+prefactor. The anharmonic prefactors have units deg^(-n), for example
+-0.014 deg^(-1), 5.6(10)^(-5) deg^(-2), ...
+
+The following coefficients must be defined for each angle type via the
+"angle_coeff"_angle_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+K (energy/radian^2)
+theta0 (degrees) :ul
+
+Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+USER_YAFF package. See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"angle_coeff"_angle_coeff.html
+
+[Default:] none
+
+:line
+
diff --git a/doc/src/angle_style.txt b/doc/src/angle_style.txt
index 2c3c1f2bd1ff81aeb8a057b42148488cd096c6be..2f2da678d86ab7a2e254e318d0b713a87381add0 100644
--- a/doc/src/angle_style.txt
+++ b/doc/src/angle_style.txt
@@ -81,10 +81,12 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
"cosine/shift"_angle_cosine_shift.html - angle cosine with a shift
"cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant
"cosine/squared"_angle_cosine_squared.html - angle with cosine squared term
+"cross"_angle_cross.html - cross term coupling angle and bond lengths
"dipole"_angle_dipole.html - angle that controls orientation of a point dipole
"fourier"_angle_fourier.html - angle with multiple cosine terms
"fourier/simple"_angle_fourier_simple.html - angle with a single cosine term
"harmonic"_angle_harmonic.html - harmonic angle
+"mm3"_angle_mm3.html - anharmonic angle
"quartic"_angle_quartic.html - angle with cubic and quartic terms
"sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms
"table"_angle_table.html - tabulated by angle :ul
diff --git a/doc/src/angles.txt b/doc/src/angles.txt
index 3e91ba9917176bf02c5e06ba403aa18b2b2cd9d6..3d8a47b2ebceb834ca91aec44d81dd42f5b4c9e2 100644
--- a/doc/src/angles.txt
+++ b/doc/src/angles.txt
@@ -14,11 +14,13 @@ Angle Styles :h1
angle_cosine_shift
angle_cosine_shift_exp
angle_cosine_squared
+ angle_cross
angle_dipole
angle_fourier
angle_fourier_simple
angle_harmonic
angle_hybrid
+ angle_mm3
angle_none
angle_quartic
angle_sdk
diff --git a/doc/src/bond_mm3.txt b/doc/src/bond_mm3.txt
new file mode 100644
index 0000000000000000000000000000000000000000..c3d0e39f52cf4885a7bd271cc00b8f60413b6163
--- /dev/null
+++ b/doc/src/bond_mm3.txt
@@ -0,0 +1,58 @@
+"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
+
+bond_style mm3 command :h3
+
+[Syntax:]
+
+bond_style mm3 :pre
+
+[Examples:]
+
+bond_style mm3
+bond_coeff 1 100.0 107.0 :pre
+
+[Description:]
+
+The {mm3} bond style uses the potential that is anharmonic in the bond
+as defined in "(Allinger)"_#mm3-allinger1989
+
+:c,image(Eqs/bond_mm3.jpg)
+
+where r0 is the equilibrium value of the bond, and K is a
+prefactor. The anharmonic prefactors have units angstrom^(-n):
+-2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes
+care of the necessary unit conversion for these factors internally.
+Note that the MM3 papers contains an error in Eq (1):
+(7/12)2.55 should be replaced with (7/12)2.55^2
+
+The following coefficients must be defined for each bond type via the
+"bond_coeff"_bond_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+K (energy/distance^2)
+r0 (distance) :ul
+
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+USER_YAFF package. See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"bond_coeff"_bond_coeff.html
+
+[Default:] none
+
+:line
+
+:link(mm3-allinger1989)
+[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
+(1989),
diff --git a/doc/src/bond_style.txt b/doc/src/bond_style.txt
index ae19f2369d83c476ea9cad4740efbb5c55968d07..aba6d3a7781fe952c7977361536ae758983654ba 100644
--- a/doc/src/bond_style.txt
+++ b/doc/src/bond_style.txt
@@ -86,6 +86,7 @@ accelerated styles exist.
"harmonic"_bond_harmonic.html - harmonic bond
"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
+"mm3"_bond_mm3.html - MM3 anharmonic bond
"morse"_bond_morse.html - Morse bond
"nonlinear"_bond_nonlinear.html - nonlinear bond
"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling
diff --git a/doc/src/bonds.txt b/doc/src/bonds.txt
index d33515eb88e36c3aca1525e5426a6cc80cbdeae8..48896e711c3bcdc57dd637c00ec0d285a6914f61 100644
--- a/doc/src/bonds.txt
+++ b/doc/src/bonds.txt
@@ -13,6 +13,7 @@ Bond Styles :h1
bond_harmonic_shift
bond_harmonic_shift_cut
bond_hybrid
+ bond_mm3
bond_morse
bond_none
bond_nonlinear
diff --git a/doc/src/improper_distharm.txt b/doc/src/improper_distharm.txt
new file mode 100644
index 0000000000000000000000000000000000000000..52815e76aaaab5226076876c2bc118e3bf9e67f4
--- /dev/null
+++ b/doc/src/improper_distharm.txt
@@ -0,0 +1,53 @@
+"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
+
+improper_style distharm command :h3
+
+[Syntax:]
+
+improper_style distharm
+
+[Examples:]
+
+improper_style distharm
+improper_coeff 1 25.0 0.5 :pre
+
+[Description:]
+
+The {distharm} improper style uses the potential
+
+:c,image(Eqs/improper_distharm.jpg)
+
+where d is the oriented distance between the central atom and the plane formed
+by the other three atoms. If the 4 atoms in an improper quadruplet
+(listed in the data file read by the "read_data"_read_data.html
+command) are ordered I,J,K,L then the L-atom is assumed to be the
+central atom. Note that this is different from the convention used
+in the improper_style distance. The distance d is oriented and can take
+on negative values. This may lead to unwanted behavior if d0 is not equal to zero.
+
+The following coefficients must be defined for each improper type via
+the improper_coeff command as in the example above, or in the data
+file or restart files read by the read_data or read_restart commands:
+
+K (energy/distance^2)
+d0 (distance) :ul
+
+:line
+
+[Restrictions:]
+
+This improper style can only be used if LAMMPS was built with the
+USER-YAFF package. See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"improper_coeff"_improper_coeff.html
+
+[Default:] none
diff --git a/doc/src/improper_sqdistharm.txt b/doc/src/improper_sqdistharm.txt
new file mode 100644
index 0000000000000000000000000000000000000000..7473fd8c5d87ed15c26ecfe9fba0dec3d92c0642
--- /dev/null
+++ b/doc/src/improper_sqdistharm.txt
@@ -0,0 +1,54 @@
+"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
+
+improper_style sqdistharm command :h3
+
+[Syntax:]
+
+improper_style sqdistharm
+
+[Examples:]
+
+improper_style sqdistharm
+improper_coeff 1 50.0 0.1 :pre
+
+[Description:]
+
+The {sqdistharm} improper style uses the potential
+
+:c,image(Eqs/improper_sqdistharm.jpg)
+
+where d is the distance between the central atom and the plane formed
+by the other three atoms. If the 4 atoms in an improper quadruplet
+(listed in the data file read by the "read_data"_read_data.html
+command) are ordered I,J,K,L then the L-atom is assumed to be the
+central atom. Note that this is different from the convention used
+in the improper_style distance.
+
+The following coefficients must be defined for each improper type via
+the improper_coeff command as in the example above, or in the data
+file or restart files read by the read_data or read_restart commands:
+
+K (energy/distance^4)
+d0^2 (distance^2) :ul
+
+Note that d0^2 (in units distance^2) has be provided and not d0.
+
+:line
+
+[Restrictions:]
+
+This improper style can only be used if LAMMPS was built with the
+USER-MISC package. See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"improper_coeff"_improper_coeff.html
+
+[Default:] none
diff --git a/doc/src/improper_style.txt b/doc/src/improper_style.txt
index c5e0be8a819aac165d61952af8abee28b908a22c..cd72da4d073d700aef9d310a1f2aa362334b651f 100644
--- a/doc/src/improper_style.txt
+++ b/doc/src/improper_style.txt
@@ -78,11 +78,13 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist.
"cossq"_improper_cossq.html - improper with a cosine squared term
"cvff"_improper_cvff.html - CVFF improper
"distance"_improper_distance.html - improper based on distance between atom planes
+"distharm"_improper_distharm.html - improper that is harmonic in the out-of-plane distance
"fourier"_improper_fourier.html - improper with multiple cosine terms
"harmonic"_improper_harmonic.html - harmonic improper
"inversion/harmonic"_improper_inversion_harmonic.html - harmonic improper with Wilson-Decius out-of-plane definition
"ring"_improper_ring.html - improper which prevents planar conformations
"umbrella"_improper_umbrella.html - DREIDING improper :ul
+"sqdistharm"_improper_sqdistharm.html - improper that is harmonic in the square of the out-of-plane distance
:line
diff --git a/doc/src/impropers.txt b/doc/src/impropers.txt
index ca6c839c95a03fc934d8811d8e4ab0284f4b2d94..ce829197fe8d5970a6c13752d116145db281ae03 100644
--- a/doc/src/impropers.txt
+++ b/doc/src/impropers.txt
@@ -9,6 +9,7 @@ Improper Styles :h1
improper_cossq
improper_cvff
improper_distance
+ improper_distharm
improper_fourier
improper_harmonic
improper_hybrid
@@ -16,6 +17,7 @@ Improper Styles :h1
improper_none
improper_ring
improper_umbrella
+ improper_sqdistharm
improper_zero
END_RST -->
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index a1bbaf896ed48258a7d75f6257acc8d941f82f4e..5ae3456ad4be214edce5fc66e0d55b4e6418db26 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -596,6 +596,7 @@ pair_lj_long.html
pair_lj_smooth.html
pair_lj_smooth_linear.html
pair_lj_soft.html
+pair_lj_switch3_coulgauss.html
pair_lubricate.html
pair_lubricateU.html
pair_mdf.html
@@ -605,6 +606,7 @@ pair_meam_sw_spline.html
pair_meso.html
pair_mgpt.html
pair_mie.html
+pair_mm3_switch3_coulgauss.html
pair_momb.html
pair_morse.html
pair_multi_lucy.html
@@ -668,6 +670,7 @@ bond_harmonic_shift.html
bond_harmonic_shift_cut.html
bond_hybrid.html
bond_morse.html
+bond_mm3.html
bond_none.html
bond_nonlinear.html
bond_oxdna.html
@@ -687,11 +690,13 @@ angle_cosine_periodic.html
angle_cosine_shift.html
angle_cosine_shift_exp.html
angle_cosine_squared.html
+angle_cross.html
angle_dipole.html
angle_fourier.html
angle_fourier_simple.html
angle_harmonic.html
angle_hybrid.html
+angle_mm3.html
angle_none.html
angle_quartic.html
angle_sdk.html
@@ -725,6 +730,7 @@ improper_class2.html
improper_cossq.html
improper_cvff.html
improper_distance.html
+improper_distharm.html
improper_fourier.html
improper_harmonic.html
improper_hybrid.html
@@ -732,6 +738,7 @@ improper_inversion_harmonic.html
improper_none.html
improper_ring.html
improper_umbrella.html
+improper_sqdistharm.html
improper_zero.html
lammps_commands_kspace.html
diff --git a/doc/src/pair_lj_switch3_coulgauss.txt b/doc/src/pair_lj_switch3_coulgauss.txt
new file mode 100644
index 0000000000000000000000000000000000000000..1277cff9aa995ed3663050dd966729ac42db6a17
--- /dev/null
+++ b/doc/src/pair_lj_switch3_coulgauss.txt
@@ -0,0 +1,86 @@
+"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 lj/switch3/coulgauss/long command :h3
+
+[Syntax:]
+
+pair_style style args :pre
+
+style = {lj/switch3/coulgauss/long}
+args = list of arguments for a particular style :ul
+ {lj/switch3/coulgauss/long} args = cutoff (cutoff2) width
+ cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ width = width parameter of the smoothing function (distance units) :pre
+
+[Examples:]
+
+pair_style lj/switch3/coulgauss/long 12.0 3.0
+pair_coeff 1 0.2 2.5 1.2 :pre
+
+pair_style lj/switch3/coulgauss/long 12.0 10.0 3.0
+pair_coeff 1 0.2 2.5 1.2 :pre
+
+[Description:]
+
+The {lj/switch3/coulgauss} style evaluates the LJ
+vdW potential
+
+:c,image(Eqs/pair_lj_switch3.jpg)
+
+, which goes smoothly to zero at the cutoff r_c as defined
+by the switching function
+
+:c,image(Eqs/pair_switch3.jpg)
+
+where w is the width defined in the arguments. This potential
+is combined with Coulomb interaction between Gaussian charge densities:
+
+:c,image(Eqs/pair_coulgauss.jpg)
+
+where qi and qj are the
+charges on the 2 atoms, epsilon is the dielectric constant which
+can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j
+are the widths of the Gaussian charge distribution and erf() is the error-function.
+This style has to be used in conjunction with the "kspace_style"_kspace_style.html command
+
+If one cutoff is specified it is used for both the vdW and Coulomb
+terms. If two cutoffs are specified, the first is used as the cutoff
+for the vdW terms, and the second is the cutoff for the Coulombic term.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html
+commands:
+
+epsilon (energy)
+sigma (distance)
+gamma (distance) :ul
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+Shifting the potential energy is not necessary because the switching
+function ensures that the potential is zero at the cut-off.
+
+
+[Restrictions:]
+
+These styles are part of the USER-YAFF package. They are only
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
diff --git a/doc/src/pair_mm3_switch3_coulgauss.txt b/doc/src/pair_mm3_switch3_coulgauss.txt
new file mode 100644
index 0000000000000000000000000000000000000000..3e0e24150e2c1e2a8f11ee8eb085599797ebfc1c
--- /dev/null
+++ b/doc/src/pair_mm3_switch3_coulgauss.txt
@@ -0,0 +1,88 @@
+"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 mm3/switch3/coulgauss/long command :h3
+
+[Syntax:]
+
+pair_style style args :pre
+
+style = {mm3/switch3/coulgauss/long}
+args = list of arguments for a particular style :ul
+ {mm3/switch3/coulgauss/long} args = cutoff (cutoff2) width
+ cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
+ cutoff2 = global cutoff for Coulombic (optional) (distance units)
+ width = width parameter of the smoothing function (distance units) :pre
+
+[Examples:]
+
+pair_style mm3/switch3/coulgauss/long 12.0 3.0
+pair_coeff 1 0.2 2.5 1.2 :pre
+
+pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0
+pair_coeff 1 0.2 2.5 1.2 :pre
+
+[Description:]
+
+The {mm3/switch3/coulgauss} style evaluates the MM3
+vdW potential "(Allinger)"_#mm3-allinger1989
+
+:c,image(Eqs/pair_mm3_switch3.jpg)
+
+, which goes smoothly to zero at the cutoff r_c as defined
+by the switching function
+
+:c,image(Eqs/pair_switch3.jpg)
+
+where w is the width defined in the arguments. This potential
+is combined with Coulomb interaction between Gaussian charge densities:
+
+:c,image(Eqs/pair_coulgauss.jpg)
+
+where qi and qj are the
+charges on the 2 atoms, epsilon is the dielectric constant which
+can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j
+are the widths of the Gaussian charge distribution and erf() is the error-function.
+This style has to be used in conjunction with the "kspace_style"_kspace_style.html command
+
+If one cutoff is specified it is used for both the vdW and Coulomb
+terms. If two cutoffs are specified, the first is used as the cutoff
+for the vdW terms, and the second is the cutoff for the Coulombic term.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html
+commands:
+
+epsilon (energy)
+r_v (distance)
+gamma (distance) :ul
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+Mixing rules are fixed for this style as defined above.
+
+Shifting the potential energy is not necessary because the switching
+function ensures that the potential is zero at the cut-off.
+
+
+[Restrictions:]
+
+These styles are part of the USER-YAFF package. They are only
+enabled if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
index 714ec55d2e115a9affe382f2a6aca1e8b44b2a0b..978277245607446d9a1abb3214dfbc6949035276 100644
--- a/doc/src/pair_style.txt
+++ b/doc/src/pair_style.txt
@@ -220,6 +220,7 @@ accelerated styles exist.
"lj/sf/dipole/sf"_pair_dipole.html - LJ with dipole interaction with shifted forces
"lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed LJ potential
+"lj/switch3/coulgauss"_pair_lj_switch3_coulgauss - smoothed LJ vdW potential with Gaussian electrostatics
"lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
"lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
"lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity
@@ -232,6 +233,7 @@ accelerated styles exist.
"meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term
"mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential
"mie/cut"_pair_mie.html - Mie potential
+"mm3/switch3/coulgauss"_pair_mm3_switch3_coulgauss - smoothed MM3 vdW potential with Gaussian electrostatics
"momb"_pair_momb.html - Many-Body Metal-Organic (MOMB) force field
"morse"_pair_morse.html - Morse potential
"morse/smooth/linear"_pair_morse.html - linear smoothed Morse potential
diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
index 281025240246728ab73f4f244dbefa5e63e1d1aa..62cbb7f56d018662c260feae935e7343994b1453 100644
--- a/doc/src/pairs.txt
+++ b/doc/src/pairs.txt
@@ -61,6 +61,7 @@ Pair Styles :h1
pair_lj_smooth
pair_lj_smooth_linear
pair_lj_soft
+ pair_lj_switch3_coulgauss
pair_lubricate
pair_lubricateU
pair_mdf
@@ -70,6 +71,7 @@ Pair Styles :h1
pair_meso
pair_mgpt
pair_mie
+ pair_mm3_switch3_coulgauss
pair_momb
pair_morse
pair_multi_lucy
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 5c44bf8afacabf5f89be643111740ec4f2a7279f..8807b2d680766839db90849a37662f5f53d02b6d 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -60,6 +60,7 @@ Alejandre
alessandro
Alessandro
aliceblue
+Allinger
allocaters
allosws
AlO
@@ -410,6 +411,7 @@ cossq
costheta
Couette
coul
+coulgauss
coulombic
Coulombic
Coulombics
@@ -566,6 +568,7 @@ discretized
disp
dissipative
Dissipative
+distharm
dl
dlambda
DLAMMPS
@@ -2493,6 +2496,7 @@ Springer
springgreen
spx
spz
+sqdistharm
sqrt
src
srd
@@ -2801,6 +2805,8 @@ Valone
valuev
Valuev
Vanden
+Vandenbrande
+Vanduyfhuys
varavg
Varshalovich
Varshney
@@ -2958,6 +2964,8 @@ xy
xyz
xz
xzhou
+YAFF
+yaff
Yamada
Yazdani
Ybar
@@ -2976,6 +2984,7 @@ ys
ysu
yu
Yu
+Yuh
yukawa
Yukawa
Yusof
diff --git a/examples/USER/yaff/README b/examples/USER/yaff/README
new file mode 100644
index 0000000000000000000000000000000000000000..af43a61e0842c6e80369daab2d997ad1f54677dc
--- /dev/null
+++ b/examples/USER/yaff/README
@@ -0,0 +1,7 @@
+mof5:
+ NPT simulation of MOF5 using a QuickFF force field
+
+mil53al:
+ NPT simulation of MIL-53(Al) using a QuickFF force field.
+ If the pressure is high enough (for instance 2000 atm),
+ a phase transition from large pore to narrow pore is observed
diff --git a/examples/USER/yaff/mil53al/lammps.data b/examples/USER/yaff/mil53al/lammps.data
new file mode 100644
index 0000000000000000000000000000000000000000..7b73c99357e3caa3472acc08ebf4d33a324e935b
--- /dev/null
+++ b/examples/USER/yaff/mil53al/lammps.data
@@ -0,0 +1,1545 @@
+Generated by yaff2lammps
+
+ 152 atoms
+ 184 bonds
+ 736 angles
+ 288 dihedrals
+ 64 impropers
+
+ 8 atom types
+ 8 bond types
+ 34 angle types
+ 9 dihedral types
+ 3 improper types
+
+ 0.0000000000000000000000000000000000 13.3259954452999984653160936431959271 xlo xhi
+ 0.0000000000000000000000000000000000 17.0769005354000000806991010904312134 ylo yhi
+ 0.0000000000000000000000000000000000 12.5451650575000002163505996577441692 zlo zhi
+ 0.2406519637999999794431005284423009 -0.0003290864999999999263892436207612 0.0000597691999999999968857904153463 xy xz yz
+
+Masses
+
+ 1 15.99940000 # O_HY
+ 2 15.99940000 # O_CA
+ 3 1.00794000 # H_HY
+ 4 1.00794000 # H_PH
+ 5 26.98153860 # AL
+ 6 12.01070000 # C_PH
+ 7 12.01070000 # C_PC
+ 8 12.01070000 # C_CA
+
+Bond Coeffs
+
+ 1 567.89714613 0.99006574
+ 2 149.93642745 1.86984652
+ 3 111.04240192 1.91161348
+ 4 389.90538840 1.09141352
+ 5 491.67603879 1.38895490
+ 6 451.37211172 1.40304450
+ 7 668.04674737 1.27972749
+ 8 320.55756064 1.49110450
+
+Angle Coeffs
+
+ 1 cosine/periodic 2.83639133 1 4
+ 2 cross 6.00819953 13.51503788 20.21646410 1.85789452 0.98840688 111.64709450
+ 3 cross 6.00819953 20.21646410 13.51503788 0.98840688 1.85789452 111.64709450
+ 4 cross 44.73850113 10.65965583 10.65965583 1.85789452 1.85789452 128.05371526
+ 5 cross 79.26686011 18.67531488 42.84377495 1.90495331 1.27905582 132.82471928
+ 6 cross 79.26686011 42.84377495 18.67531488 1.27905582 1.90495331 132.82471928
+ 7 cross -6.85938357 0.00000000 0.00000000 1.85789452 1.85789452 0.00000000
+ 8 cross 20.15880651 47.33122583 34.90884408 1.90495331 1.85789452 89.96038503
+ 9 cross 20.15880651 34.90884408 47.33122583 1.85789452 1.90495331 89.96038503
+ 10 cross 26.34746514 0.00000000 0.00000000 1.90495331 1.90495331 0.00000000
+ 11 cross 29.49811022 32.88373608 17.10597622 1.09150478 1.40308083 119.48992692
+ 12 cross 29.49811022 17.10597622 32.88373608 1.40308083 1.09150478 119.48992692
+ 13 cross 130.12394367 9.80817840 18.96121618 1.40308083 1.38855980 120.04435536
+ 14 cross 130.12394367 18.96121618 9.80817840 1.38855980 1.40308083 120.04435536
+ 15 cross 26.93982909 21.36148219 26.91818347 1.38855980 1.09150478 120.51713090
+ 16 cross 26.93982909 26.91818347 21.36148219 1.09150478 1.38855980 120.51713090
+ 17 cross 69.39565871 31.02625485 12.91121121 1.49380304 1.40308083 120.04236743
+ 18 cross 69.39565871 12.91121121 31.02625485 1.40308083 1.49380304 120.04236743
+ 19 cross 132.39591455 8.36520076 8.36520076 1.40308083 1.40308083 119.90683966
+ 20 cross 101.87765421 105.70691653 47.75221042 1.27905582 1.49380304 117.59476167
+ 21 cross 101.87765421 47.75221042 105.70691653 1.49380304 1.27905582 117.59476167
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+ 30 harmonic 43.33676649 120.04493381
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+ 33 harmonic 76.76979213 124.86144100
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+Improper Coeffs
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+ 1 9.10278571 0.00000000
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+Pair Coeffs
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+ 1 0.059000000000 1.820000000000 1.132500000000 # O_HY
+ 2 0.059000000000 1.820000000000 1.132500000000 # O_CA
+ 3 0.016000000000 1.600000000000 0.730800000000 # H_HY
+ 4 0.020000000000 1.620000000000 0.730800000000 # H_PH
+ 5 0.116000000000 2.360000000000 1.674200000000 # AL
+ 6 0.056000000000 1.940000000000 1.170300000000 # C_PH
+ 7 0.056000000000 1.940000000000 1.170300000000 # C_PC
+ 8 0.056000000000 1.940000000000 1.170300000000 # C_CA
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+
+Dihedrals
+
+ 1 4 125 93 89 49
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+
+Impropers
+
+ 1 3 89 49 122 93
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+ 60 2 148 20 132 40
+ 61 2 149 33 133 22
+ 62 2 150 34 21 134
+ 63 2 151 35 135 23
+ 64 2 152 36 136 24
diff --git a/examples/USER/yaff/mil53al/lammps.in b/examples/USER/yaff/mil53al/lammps.in
new file mode 100644
index 0000000000000000000000000000000000000000..a2b6329bbdfe433d858a1e29591e1f8f4d45447e
--- /dev/null
+++ b/examples/USER/yaff/mil53al/lammps.in
@@ -0,0 +1,42 @@
+#########################################
+#General settings
+#########################################
+units real
+atom_style full
+boundary p p p
+dielectric 1
+
+#########################################
+#Force field and system specification
+#########################################
+special_bonds lj 0.000000 0.000000 1.000000 coul 1.000000 1.000000 1.000000
+pair_style mm3/switch3/coulgauss/long 12.0000 4.0000
+pair_modify table 16 # Accuracy of the table used for real space electrostatics
+pair_modify mix arithmetic
+pair_modify tail no
+bond_style harmonic
+angle_style hybrid cosine/periodic cross harmonic cosine/squared
+dihedral_style fourier
+improper_style distharm
+box tilt large
+
+read_data lammps.data # Data file location
+kspace_style pppm 0.0000001 # Ewald accuracy
+neighbor 2.0 multi
+neigh_modify every 2 delay 4 check yes
+
+#########################################
+#Output settings
+#########################################
+thermo 100 # Provide output every n steps
+thermo_style custom step time etotal ke temp pe emol evdwl ecoul elong etail vol press
+thermo_modify line multi format float %20.12f
+
+#########################################
+#Sampling options
+#########################################
+timestep 0.5 # in femtosecond
+velocity all create 0.0 5 # initial temperature in Kelvin and random seed
+fix 1 all npt temp 300.0 300.0 100.0 tri 2000.0 2000.0 1000.0 tchain 3 mtk yes nreset 1000
+fix_modify 1 energy yes # Add thermo/barostat contributions to energy
+run 10000
diff --git a/examples/USER/yaff/mof5/lammps.data b/examples/USER/yaff/mof5/lammps.data
new file mode 100644
index 0000000000000000000000000000000000000000..acc6f7d3d22392d1a958101adb3f65dd2811888f
--- /dev/null
+++ b/examples/USER/yaff/mof5/lammps.data
@@ -0,0 +1,4315 @@
+Generated by yaff2lammps
+
+ 424 atoms
+ 512 bonds
+ 1824 angles
+ 1248 dihedrals
+ 192 impropers
+
+ 7 atom types
+ 7 bond types
+ 29 angle types
+ 11 dihedral types
+ 3 improper types
+
+ 0.0000000000000000000000000000000000 26.4070248643267468935391661943867803 xlo xhi
+ 0.0000000000000000000000000000000000 26.4070252891212220447414438240230083 ylo yhi
+ 0.0000000000000000000000000000000000 26.4070257154843517355402582325041294 zlo zhi
+ -0.0000000007111492372846892652846758 -0.0000000000659408828932501509572980 -0.0000000000464737531820980317620204 xy xz yz
+
+Masses
+
+ 1 65.40900000 # Zn
+ 2 15.99940000 # O_CE
+ 3 15.99940000 # O_CA
+ 4 12.01070000 # C_CA
+ 5 12.01070000 # C_PH
+ 6 12.01070000 # C_PC
+ 7 1.00794000 # H_PH
+
+Bond Coeffs
+
+ 1 682.36094515 1.27102391
+ 2 499.48089314 1.38650552
+ 3 328.64606795 1.49449724
+ 4 465.15110963 1.39880394
+ 5 406.68075027 1.08330871
+ 6 107.02127303 2.03268653
+ 7 113.67644184 1.98848069
+
+Angle Coeffs
+
+ 1 cross 193.48062339 101.27328163 101.27328163 1.27218805 1.27218805 123.91120600
+ 2 cross 90.86010618 104.60333096 43.56504880 1.27186911 1.49086906 118.21448172
+ 3 cross 90.86010618 43.56504880 104.60333096 1.49086906 1.27186911 118.21448172
+ 4 cross 130.81104940 12.67739461 16.17645862 1.39837427 1.38759779 120.07946149
+ 5 cross 130.81104940 16.17645862 12.67739461 1.38759779 1.39837427 120.07946149
+ 6 cross 11.41676921 30.63883886 25.17734414 1.08331485 1.39837427 119.52155527
+ 7 cross 11.41676921 25.17734414 30.63883886 1.39837427 1.08331485 119.52155527
+ 8 cross 12.44667401 28.35704887 28.27577085 1.38759779 1.08331485 120.41324047
+ 9 cross 12.44667401 28.27577085 28.35704887 1.08331485 1.38759779 120.41324047
+ 10 cross 75.95522848 37.17414513 10.05189907 1.49086906 1.39837427 119.94754556
+ 11 cross 75.95522848 10.05189907 37.17414513 1.39837427 1.49086906 119.94754556
+ 12 cross 144.65705708 -7.34407121 -7.34407121 1.39837427 1.39837427 119.90241395
+ 13 cross 20.17000841 2.28355442 -7.92322284 1.98727825 2.03828701 109.42277782
+ 14 cross 20.17000841 -7.92322284 2.28355442 2.03828701 1.98727825 109.42277782
+ 15 cross 22.09014578 27.25520258 27.25520258 1.98727825 1.98727825 108.41474547
+ 16 cross 35.09855972 13.51120456 13.51120456 2.03828701 2.03828701 110.23699695
+ 17 cross 60.09401332 6.52883112 6.33031133 1.27250698 1.98727825 133.24307044
+ 18 cross 60.09401332 6.33031133 6.52883112 1.98727825 1.27250698 133.24307044
+ 19 mm3 89.55892156 124.04066786
+ 20 mm3 66.99975548 120.08429731
+ 21 mm3 36.80738383 120.34964823
+ 22 mm3 78.98317285 118.11635047
+ 23 mm3 45.56202376 120.27481067
+ 24 mm3 38.05295940 119.66571944
+ 25 mm3 69.51816469 119.99726194
+ 26 mm3 10.37923783 135.02173615
+ 27 mm3 7.08946285 108.92035063
+ 28 mm3 9.10447143 107.51166462
+ 29 mm3 29.71892770 109.45766072
+
+Dihedral Coeffs
+
+ 1 1 3.64767899 2 -180.00000000
+ 2 1 2.35495004 2 -180.00000000
+ 3 1 0.77392291 2 -180.00000000
+ 4 1 4.23729765 2 -180.00000000
+ 5 1 3.96491674 2 -180.00000000
+ 6 1 3.27183804 2 -180.00000000
+ 7 1 2.21748040 2 -180.00000000
+ 8 1 5.15273943 2 -180.00000000
+ 9 1 0.07197799 2 -180.00000000
+ 10 1 1.18073306 2 -180.00000000
+ 11 1 0.13801067 3 -180.00000000
+
+Improper Coeffs
+
+ 1 27.54315214 0.30000000
+ 2 196.72513766 0.20000000
+ 3 21.31242806 0.10000000
+
+Pair Coeffs
+
+ 1 0.276000000000 2.290000000000 2.073000000000 # Zn
+ 2 0.059000000000 1.820000000000 1.132500000000 # O_CE
+ 3 0.059000000000 1.820000000000 1.132500000000 # O_CA
+ 4 0.056000000000 1.940000000000 1.164600000000 # C_CA
+ 5 0.056000000000 1.960000000000 1.164600000000 # C_PH
+ 6 0.056000000000 1.960000000000 1.164600000000 # C_PC
+ 7 0.020000000000 1.620000000000 0.730900000000 # H_PH
+
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+
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+
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diff --git a/examples/USER/yaff/mof5/lammps.in b/examples/USER/yaff/mof5/lammps.in
new file mode 100644
index 0000000000000000000000000000000000000000..1decfd77e4d67fea6a4b3ff9019ecf0a8641425e
--- /dev/null
+++ b/examples/USER/yaff/mof5/lammps.in
@@ -0,0 +1,42 @@
+#########################################
+#General settings
+#########################################
+units real
+atom_style full
+boundary p p p
+dielectric 1
+
+#########################################
+#Force field and system specification
+#########################################
+special_bonds lj 0.000000 0.000000 1.000000 coul 1.000000 1.000000 1.000000
+pair_style mm3/switch3/coulgauss/long 12.0000 4.0000
+pair_modify table 16 # Accuracy of the table used for real space electrostatics
+pair_modify mix arithmetic
+pair_modify tail no
+bond_style mm3
+angle_style hybrid cross mm3
+dihedral_style fourier
+improper_style distharm
+box tilt large
+
+read_data lammps.data # Data file location
+kspace_style pppm 0.0000001 # Ewald accuracy
+neighbor 2.0 multi
+neigh_modify every 2 delay 4 check yes
+
+#########################################
+#Output settings
+#########################################
+thermo 10 # Provide output every n steps
+thermo_style custom step time etotal ke temp pe emol evdwl ecoul elong etail vol press
+thermo_modify line multi format float %20.12f
+
+#########################################
+#Sampling options
+#########################################
+timestep 0.5 # in femtosecond
+velocity all create 0.0 5 # initial temperature in Kelvin and random seed
+fix 1 all npt temp 300.0 300.0 100.0 tri 1.0 1.0 1000.0 tchain 3 mtk yes nreset 1000
+fix_modify 1 energy yes # Add thermo/barostat contributions to energy
+run 100
diff --git a/src/Makefile b/src/Makefile
index c58d5bd9eb0be6ccae0339d65bb602cf4b6468fe..ee3159b588bf2775b969f3ec2fe2bd2aff9ead61 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -63,7 +63,7 @@ PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-mgpt user-misc user-mofff user-molfile \
user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \
user-qtb user-quip user-reaxc user-scafacos user-smd user-smtbq \
- user-sdpd user-sph user-tally user-uef user-vtk
+ user-sdpd user-sph user-tally user-uef user-vtk user-yaff
PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \
python voronoi \
diff --git a/src/USER-YAFF/README b/src/USER-YAFF/README
new file mode 100644
index 0000000000000000000000000000000000000000..4fabe6739066591b0cbc1de0cf0bfbed9afd16f8
--- /dev/null
+++ b/src/USER-YAFF/README
@@ -0,0 +1,8 @@
+This package implements the styles that are needed to use typical force fields
+generated by QuickFF for the simulation of metal-organic frameworks. The
+QuickFF methodology is detailed in following papers:
+ Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) http://dx.doi.org/10.1002/jcc.23877
+ Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) http://dx.doi.org/10.1002/jcc.25173
+The corresponding software package can be found on http://molmod.github.io/QuickFF
+
+
diff --git a/src/USER-YAFF/angle_cross.cpp b/src/USER-YAFF/angle_cross.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..a31931a23b429078628b01ba4c9af3d0a0875667
--- /dev/null
+++ b/src/USER-YAFF/angle_cross.cpp
@@ -0,0 +1,344 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Steven Vandenbrande
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
+#include "angle_cross.h"
+#include "atom.h"
+#include "neighbor.h"
+#include "domain.h"
+#include "comm.h"
+#include "force.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define SMALL 0.001
+
+/* ---------------------------------------------------------------------- */
+
+AngleCross::AngleCross(LAMMPS *lmp) : Angle(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+AngleCross::~AngleCross()
+{
+ if (copymode) return;
+
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(kss);
+ memory->destroy(kbs0);
+ memory->destroy(kbs1);
+ memory->destroy(r00);
+ memory->destroy(r01);
+ memory->destroy(theta0);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AngleCross::compute(int eflag, int vflag)
+{
+ int i1,i2,i3,n,type;
+ double delx1,dely1,delz1,delx2,dely2,delz2;
+ double eangle,f1[3],f3[3];
+ double dtheta,dtheta2,dtheta3,dtheta4,de_angle;
+ double dr1,dr2,tk1,tk2,aa1,aa2,aa11,aa12,aa21,aa22;
+ double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22,b1,b2;
+ double vx11,vx12,vy11,vy12,vz11,vz12,vx21,vx22,vy21,vy22,vz21,vz22;
+
+ eangle = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int **anglelist = neighbor->anglelist;
+ int nanglelist = neighbor->nanglelist;
+ int nlocal = atom->nlocal;
+ int newton_bond = force->newton_bond;
+
+ for (n = 0; n < nanglelist; n++) {
+ i1 = anglelist[n][0];
+ i2 = anglelist[n][1];
+ i3 = anglelist[n][2];
+ type = anglelist[n][3];
+
+ // 1st bond
+
+ delx1 = x[i1][0] - x[i2][0];
+ dely1 = x[i1][1] - x[i2][1];
+ delz1 = x[i1][2] - x[i2][2];
+
+ rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
+ r1 = sqrt(rsq1);
+
+ // 2nd bond
+
+ delx2 = x[i3][0] - x[i2][0];
+ dely2 = x[i3][1] - x[i2][1];
+ delz2 = x[i3][2] - x[i2][2];
+
+ rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
+ r2 = sqrt(rsq2);
+
+ // angle (cos and sin)
+
+ c = delx1*delx2 + dely1*dely2 + delz1*delz2;
+ c /= r1*r2;
+
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+
+ s = sqrt(1.0 - c*c);
+ if (s < SMALL) s = SMALL;
+ s = 1.0/s;
+
+ // force & energy for bond-bond term
+ dr1 = r1 - r00[type];
+ dr2 = r2 - r01[type];
+ tk1 = kss[type] * dr1;
+ tk2 = kss[type] * dr2;
+
+ f1[0] = -delx1*tk2/r1;
+ f1[1] = -dely1*tk2/r1;
+ f1[2] = -delz1*tk2/r1;
+
+ f3[0] = -delx2*tk1/r2;
+ f3[1] = -dely2*tk1/r2;
+ f3[2] = -delz2*tk1/r2;
+
+ if (eflag) eangle = kss[type]*dr1*dr2;
+
+ // force & energy for bond-angle term
+ dtheta = acos(c) - theta0[type];
+
+ aa1 = s * dr1 * kbs0[type];
+ aa2 = s * dr2 * kbs1[type];
+
+ aa11 = aa1 * c / rsq1;
+ aa12 = -aa1 / (r1 * r2);
+ aa21 = aa2 * c / rsq1;
+ aa22 = -aa2 / (r1 * r2);
+
+ vx11 = (aa11 * delx1) + (aa12 * delx2);
+ vx12 = (aa21 * delx1) + (aa22 * delx2);
+ vy11 = (aa11 * dely1) + (aa12 * dely2);
+ vy12 = (aa21 * dely1) + (aa22 * dely2);
+ vz11 = (aa11 * delz1) + (aa12 * delz2);
+ vz12 = (aa21 * delz1) + (aa22 * delz2);
+
+ aa11 = aa1 * c / rsq2;
+ aa21 = aa2 * c / rsq2;
+
+ vx21 = (aa11 * delx2) + (aa12 * delx1);
+ vx22 = (aa21 * delx2) + (aa22 * delx1);
+ vy21 = (aa11 * dely2) + (aa12 * dely1);
+ vy22 = (aa21 * dely2) + (aa22 * dely1);
+ vz21 = (aa11 * delz2) + (aa12 * delz1);
+ vz22 = (aa21 * delz2) + (aa22 * delz1);
+
+ b1 = kbs0[type] * dtheta / r1;
+ b2 = kbs1[type] * dtheta / r2;
+
+ f1[0] -= vx11 + b1*delx1 + vx12;
+ f1[1] -= vy11 + b1*dely1 + vy12;
+ f1[2] -= vz11 + b1*delz1 + vz12;
+
+ f3[0] -= vx21 + b2*delx2 + vx22;
+ f3[1] -= vy21 + b2*dely2 + vy22;
+ f3[2] -= vz21 + b2*delz2 + vz22;
+
+ if (eflag) eangle += kbs0[type]*dr1*dtheta + kbs1[type]*dr2*dtheta;
+
+ // apply force to each of 3 atoms
+
+ if (newton_bond || i1 < nlocal) {
+ f[i1][0] += f1[0];
+ f[i1][1] += f1[1];
+ f[i1][2] += f1[2];
+ }
+
+ if (newton_bond || i2 < nlocal) {
+ f[i2][0] -= f1[0] + f3[0];
+ f[i2][1] -= f1[1] + f3[1];
+ f[i2][2] -= f1[2] + f3[2];
+ }
+
+ if (newton_bond || i3 < nlocal) {
+ f[i3][0] += f3[0];
+ f[i3][1] += f3[1];
+ f[i3][2] += f3[2];
+ }
+
+ if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
+ delx1,dely1,delz1,delx2,dely2,delz2);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AngleCross::allocate()
+{
+ allocated = 1;
+ int n = atom->nangletypes;
+
+ memory->create(kss,n+1,"angle:kss");
+ memory->create(kbs0,n+1,"angle:kbs0");
+ memory->create(kbs1,n+1,"angle:kbs1");
+ memory->create(r00,n+1,"angle:r00");
+ memory->create(r01,n+1,"angle:r01");
+ memory->create(theta0,n+1,"angle:theta0");
+ memory->create(setflag,n+1,"angle:setflag");
+
+ for (int i = 1; i <= n; i++)
+ setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs
+------------------------------------------------------------------------- */
+
+void AngleCross::coeff(int narg, char **arg)
+{
+ if (narg != 7) error->all(FLERR,"Incorrect args for angle coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi;
+ force->bounds(FLERR,arg[0],atom->nangletypes,ilo,ihi);
+
+ int count = 0;
+
+ double kss_one = force->numeric(FLERR,arg[1]);
+ double kbs0_one = force->numeric(FLERR,arg[2]);
+ double kbs1_one = force->numeric(FLERR,arg[3]);
+ double r0_one = force->numeric(FLERR,arg[4]);
+ double r1_one = force->numeric(FLERR,arg[5]);
+ double theta0_one = force->numeric(FLERR,arg[6]);
+
+ for (int i = ilo; i <= ihi; i++) {
+ kss[i] = kss_one;
+ kbs0[i] = kbs0_one;
+ kbs1[i] = kbs1_one;
+ r00[i] = r0_one;
+ r01[i] = r1_one;
+ // Convert theta0 from degrees to radians
+ theta0[i] = theta0_one*MY_PI/180.0;
+ setflag[i] = 1;
+ count++;
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
+}
+
+/* ---------------------------------------------------------------------- */
+
+double AngleCross::equilibrium_angle(int i)
+{
+ return theta0[i];
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void AngleCross::write_restart(FILE *fp)
+{
+ fwrite(&kss[1],sizeof(double),atom->nangletypes,fp);
+ fwrite(&kbs0[1],sizeof(double),atom->nangletypes,fp);
+ fwrite(&kbs1[1],sizeof(double),atom->nangletypes,fp);
+ fwrite(&r00[1],sizeof(double),atom->nangletypes,fp);
+ fwrite(&r01[1],sizeof(double),atom->nangletypes,fp);
+ fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void AngleCross::read_restart(FILE *fp)
+{
+ allocate();
+
+ if (comm->me == 0) {
+ fread(&kss[1],sizeof(double),atom->nangletypes,fp);
+ fread(&kbs0[1],sizeof(double),atom->nangletypes,fp);
+ fread(&kbs1[1],sizeof(double),atom->nangletypes,fp);
+ fread(&r00[1],sizeof(double),atom->nangletypes,fp);
+ fread(&r01[1],sizeof(double),atom->nangletypes,fp);
+ fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
+ }
+
+ MPI_Bcast(&kss[1],atom->nangletypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&kbs0[1],atom->nangletypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&kbs1[1],atom->nangletypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&r00[1],atom->nangletypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&r01[1],atom->nangletypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
+
+ for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void AngleCross::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->nangletypes; i++)
+ fprintf(fp,"%d %g %g %g %g\n",
+ i,kss[i],kbs0[i],kbs1[i],r00[i],r01[i],theta0[i]/MY_PI*180.0);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double AngleCross::single(int type, int i1, int i2, int i3)
+{
+ double **x = atom->x;
+
+ double delx1 = x[i1][0] - x[i2][0];
+ double dely1 = x[i1][1] - x[i2][1];
+ double delz1 = x[i1][2] - x[i2][2];
+ domain->minimum_image(delx1,dely1,delz1);
+ double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
+
+ double delx2 = x[i3][0] - x[i2][0];
+ double dely2 = x[i3][1] - x[i2][1];
+ double delz2 = x[i3][2] - x[i2][2];
+ domain->minimum_image(delx2,dely2,delz2);
+ double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
+
+ double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
+ c /= r1*r2;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+
+ double s = sqrt(1.0 - c*c);
+ if (s < SMALL) s = SMALL;
+ s = 1.0/s;
+
+ double dtheta = acos(c) - theta0[type];
+ double dr1 = r1 - r00[type];
+ double dr2 = r2 - r01[type];
+ double energy = kss[type]*dr1*dr2+kbs0[type]*dr1*dtheta + kbs1[type]*dr2*dtheta;
+ return energy;
+}
diff --git a/src/USER-YAFF/angle_cross.h b/src/USER-YAFF/angle_cross.h
new file mode 100644
index 0000000000000000000000000000000000000000..7709c104145a4ebad853814dcadf792e9e0f5c3e
--- /dev/null
+++ b/src/USER-YAFF/angle_cross.h
@@ -0,0 +1,57 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef ANGLE_CLASS
+
+AngleStyle(cross,AngleCross)
+
+#else
+
+#ifndef LMP_ANGLE_CROSS_H
+#define LMP_ANGLE_CROSS_H
+
+#include <stdio.h>
+#include "angle.h"
+
+namespace LAMMPS_NS {
+
+class AngleCross : public Angle {
+ public:
+ AngleCross(class LAMMPS *);
+ virtual ~AngleCross();
+ virtual void compute(int, int);
+ void coeff(int, char **);
+ double equilibrium_angle(int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ void write_data(FILE *);
+ double single(int, int, int, int);
+
+ protected:
+ double *kss,*kbs0,*kbs1,*r00,*r01,*theta0;
+
+ void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Incorrect args for angle coefficients
+
+Self-explanatory. Check the input script or data file.
+
+*/
diff --git a/src/USER-YAFF/angle_mm3.cpp b/src/USER-YAFF/angle_mm3.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..ccd9b2e20ead2ec13815f3a06270805d6b316013
--- /dev/null
+++ b/src/USER-YAFF/angle_mm3.cpp
@@ -0,0 +1,288 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Steven Vandenbrande
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <string.h>
+#include <stdlib.h>
+#include "angle_mm3.h"
+#include "atom.h"
+#include "neighbor.h"
+#include "domain.h"
+#include "comm.h"
+#include "force.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define SMALL 0.001
+
+/* ---------------------------------------------------------------------- */
+
+AngleMM3::AngleMM3(LAMMPS *lmp) : Angle(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+AngleMM3::~AngleMM3()
+{
+ if (copymode) return;
+
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(theta0);
+ memory->destroy(k2);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AngleMM3::compute(int eflag, int vflag)
+{
+ int i1,i2,i3,n,type;
+ double delx1,dely1,delz1,delx2,dely2,delz2;
+ double eangle,f1[3],f3[3];
+ double dtheta,dtheta2,dtheta3,dtheta4,de_angle;
+ double dr1,dr2,tk1,tk2,aa1,aa2,aa11,aa12,aa21,aa22;
+ double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22,b1,b2;
+ double vx11,vx12,vy11,vy12,vz11,vz12,vx21,vx22,vy21,vy22,vz21,vz22;
+
+ eangle = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int **anglelist = neighbor->anglelist;
+ int nanglelist = neighbor->nanglelist;
+ int nlocal = atom->nlocal;
+ int newton_bond = force->newton_bond;
+
+ for (n = 0; n < nanglelist; n++) {
+ i1 = anglelist[n][0];
+ i2 = anglelist[n][1];
+ i3 = anglelist[n][2];
+ type = anglelist[n][3];
+
+ // 1st bond
+
+ delx1 = x[i1][0] - x[i2][0];
+ dely1 = x[i1][1] - x[i2][1];
+ delz1 = x[i1][2] - x[i2][2];
+
+ rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
+ r1 = sqrt(rsq1);
+
+ // 2nd bond
+
+ delx2 = x[i3][0] - x[i2][0];
+ dely2 = x[i3][1] - x[i2][1];
+ delz2 = x[i3][2] - x[i2][2];
+
+ rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
+ r2 = sqrt(rsq2);
+
+ // angle (cos and sin)
+
+ c = delx1*delx2 + dely1*dely2 + delz1*delz2;
+ c /= r1*r2;
+
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+
+ s = sqrt(1.0 - c*c);
+ if (s < SMALL) s = SMALL;
+ s = 1.0/s;
+
+ // force & energy for angle term
+
+ dtheta = acos(c) - theta0[type];
+ dtheta2 = dtheta*dtheta;
+ dtheta3 = dtheta2*dtheta;
+ dtheta4 = dtheta3*dtheta;
+ // MM3 angle term, taking into account that dtheta is expressed in rad
+ de_angle = 2.0*k2[type]*dtheta*(1.0-1.203211*dtheta+0.367674*dtheta2-0.3239159*dtheta3+0.711270*dtheta4);
+
+ a = -de_angle*s;
+ a11 = a*c / rsq1;
+ a12 = -a / (r1*r2);
+ a22 = a*c / rsq2;
+
+ f1[0] = a11*delx1 + a12*delx2;
+ f1[1] = a11*dely1 + a12*dely2;
+ f1[2] = a11*delz1 + a12*delz2;
+
+ f3[0] = a22*delx2 + a12*delx1;
+ f3[1] = a22*dely2 + a12*dely1;
+ f3[2] = a22*delz2 + a12*delz1;
+ // MM3 angle term, taking into account that dtheta is expressed in rad
+ if (eflag) eangle = k2[type]*dtheta2*(1.0-0.802141*dtheta+0.183837*dtheta2-0.131664*dtheta3+0.237090*dtheta4);
+
+ // apply force to each of 3 atoms
+
+ if (newton_bond || i1 < nlocal) {
+ f[i1][0] += f1[0];
+ f[i1][1] += f1[1];
+ f[i1][2] += f1[2];
+ }
+
+ if (newton_bond || i2 < nlocal) {
+ f[i2][0] -= f1[0] + f3[0];
+ f[i2][1] -= f1[1] + f3[1];
+ f[i2][2] -= f1[2] + f3[2];
+ }
+
+ if (newton_bond || i3 < nlocal) {
+ f[i3][0] += f3[0];
+ f[i3][1] += f3[1];
+ f[i3][2] += f3[2];
+ }
+
+ if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
+ delx1,dely1,delz1,delx2,dely2,delz2);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void AngleMM3::allocate()
+{
+ allocated = 1;
+ int n = atom->nangletypes;
+
+ memory->create(setflag,n+1,"angle:setflag");
+ memory->create(k2,n+1,"angle:k2");
+ memory->create(theta0,n+1,"angle:theta0");
+ for (int i = 1; i <= n; i++)
+ setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs
+ else -> Angle coeffs
+------------------------------------------------------------------------- */
+
+void AngleMM3::coeff(int narg, char **arg)
+{
+ if (narg != 3) error->all(FLERR,"Incorrect args for angle coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi;
+ force->bounds(FLERR,arg[0],atom->nangletypes,ilo,ihi);
+
+ int count = 0;
+
+ double k2_one = force->numeric(FLERR,arg[1]);
+ double theta0_one = force->numeric(FLERR,arg[2]);
+
+ // convert theta0 from degrees to radians
+
+ for (int i = ilo; i <= ihi; i++) {
+ k2[i] = k2_one;
+ theta0[i] = theta0_one/180.0 * MY_PI;
+ setflag[i] = 1;
+ count++;
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+double AngleMM3::equilibrium_angle(int i)
+{
+ return theta0[i];
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void AngleMM3::write_restart(FILE *fp)
+{
+ fwrite(&k2[1],sizeof(double),atom->nangletypes,fp);
+ fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void AngleMM3::read_restart(FILE *fp)
+{
+ allocate();
+
+ if (comm->me == 0) {
+ fread(&k2[1],sizeof(double),atom->nangletypes,fp);
+ fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
+ }
+
+ MPI_Bcast(&k2[1],atom->nangletypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
+
+ for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void AngleMM3::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->nangletypes; i++)
+ fprintf(fp,"%d %g %g\n",
+ i,k2[i],theta0[i]/MY_PI*180.0);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double AngleMM3::single(int type, int i1, int i2, int i3)
+{
+ double **x = atom->x;
+
+ double delx1 = x[i1][0] - x[i2][0];
+ double dely1 = x[i1][1] - x[i2][1];
+ double delz1 = x[i1][2] - x[i2][2];
+ domain->minimum_image(delx1,dely1,delz1);
+ double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
+
+ double delx2 = x[i3][0] - x[i2][0];
+ double dely2 = x[i3][1] - x[i2][1];
+ double delz2 = x[i3][2] - x[i2][2];
+ domain->minimum_image(delx2,dely2,delz2);
+ double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
+
+ double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
+ c /= r1*r2;
+ if (c > 1.0) c = 1.0;
+ if (c < -1.0) c = -1.0;
+
+ double s = sqrt(1.0 - c*c);
+ if (s < SMALL) s = SMALL;
+ s = 1.0/s;
+
+ double dtheta = acos(c) - theta0[type];
+ double dtheta2 = dtheta*dtheta;
+ double dtheta3 = dtheta2*dtheta;
+ double dtheta4 = dtheta3*dtheta;
+
+ double energy = k2[type]*dtheta2*(1.0-0.802141*dtheta+0.183837*dtheta2-0.131664*dtheta3+0.237090*dtheta4);
+
+ return energy;
+}
diff --git a/src/USER-YAFF/angle_mm3.h b/src/USER-YAFF/angle_mm3.h
new file mode 100644
index 0000000000000000000000000000000000000000..2d19b4d1b464e6e534dcfa9e0a0acafc0b563581
--- /dev/null
+++ b/src/USER-YAFF/angle_mm3.h
@@ -0,0 +1,57 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef ANGLE_CLASS
+
+AngleStyle(mm3,AngleMM3)
+
+#else
+
+#ifndef LMP_ANGLE_MM3_H
+#define LMP_ANGLE_MM3_H
+
+#include <stdio.h>
+#include "angle.h"
+
+namespace LAMMPS_NS {
+
+class AngleMM3 : public Angle {
+ public:
+ AngleMM3(class LAMMPS *);
+ virtual ~AngleMM3();
+ virtual void compute(int, int);
+ void coeff(int, char **);
+ double equilibrium_angle(int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ void write_data(FILE *);
+ double single(int, int, int, int);
+
+ protected:
+ double *theta0,*k2;
+
+ void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Incorrect args for angle coefficients
+
+Self-explanatory. Check the input script or data file.
+
+*/
diff --git a/src/USER-YAFF/bond_mm3.cpp b/src/USER-YAFF/bond_mm3.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..f0e4197c6bd6029c12d2e1c63b61412b60956333
--- /dev/null
+++ b/src/USER-YAFF/bond_mm3.cpp
@@ -0,0 +1,220 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Steven Vandenbrande
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <stdlib.h>
+#include "bond_mm3.h"
+#include "atom.h"
+#include "neighbor.h"
+#include "domain.h"
+#include "comm.h"
+#include "force.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+BondMM3::BondMM3(LAMMPS *lmp) : Bond(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+BondMM3::~BondMM3()
+{
+ if (copymode) return;
+
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(r0);
+ memory->destroy(k2);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondMM3::compute(int eflag, int vflag)
+{
+ int i1,i2,n,type;
+ double delx,dely,delz,ebond,fbond;
+ double rsq,r,dr,dr2,de_bond,K3,K4;
+
+ ebond = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int **bondlist = neighbor->bondlist;
+ int nbondlist = neighbor->nbondlist;
+ int nlocal = atom->nlocal;
+ int newton_bond = force->newton_bond;
+
+ /*
+ E = K(r-r0)^2 [1-2.55*(r-r0)+(7/12)*2.55^(2)*(r-r0)^2]
+ with -2.55 in angstrom^(-1) and (7/12)*2.55^(2) in angstrom^(-2)
+ These prefactors are converted here to the correct units
+ */
+ K3 = -2.55/force->angstrom;
+ K4 = 7.0/12.0*2.55*2.55/force->angstrom/force->angstrom;
+
+ for (n = 0; n < nbondlist; n++) {
+ i1 = bondlist[n][0];
+ i2 = bondlist[n][1];
+ type = bondlist[n][2];
+
+ delx = x[i1][0] - x[i2][0];
+ dely = x[i1][1] - x[i2][1];
+ delz = x[i1][2] - x[i2][2];
+
+ rsq = delx*delx + dely*dely + delz*delz;
+ r = sqrt(rsq);
+ dr = r - r0[type];
+ dr2 = dr*dr;
+
+ // force & energy
+
+ de_bond = 2.0*k2[type]*dr*(1.0 + 1.5*K3*dr + 2.0*K4*dr2);
+ if (r > 0.0) fbond = -de_bond/r;
+ else fbond = 0.0;
+
+ if (eflag) ebond = k2[type]*dr2*(1.0+K3*dr+K4*dr2);
+
+ // apply force to each of 2 atoms
+
+ if (newton_bond || i1 < nlocal) {
+ f[i1][0] += delx*fbond;
+ f[i1][1] += dely*fbond;
+ f[i1][2] += delz*fbond;
+ }
+
+ if (newton_bond || i2 < nlocal) {
+ f[i2][0] -= delx*fbond;
+ f[i2][1] -= dely*fbond;
+ f[i2][2] -= delz*fbond;
+ }
+
+ if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void BondMM3::allocate()
+{
+ allocated = 1;
+ int n = atom->nbondtypes;
+
+ memory->create(r0,n+1,"bond:r0");
+ memory->create(k2,n+1,"bond:k2");
+
+ memory->create(setflag,n+1,"bond:setflag");
+ for (int i = 1; i <= n; i++) setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs from one line in input script or data file
+------------------------------------------------------------------------- */
+
+void BondMM3::coeff(int narg, char **arg)
+{
+ if (narg != 3) error->all(FLERR,"Incorrect args for bond coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi;
+ force->bounds(FLERR,arg[0],atom->nbondtypes,ilo,ihi);
+
+ double k2_one = force->numeric(FLERR,arg[1]);
+ double r0_one = force->numeric(FLERR,arg[2]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ k2[i] = k2_one;
+ r0[i] = r0_one;
+ setflag[i] = 1;
+ count++;
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ return an equilbrium bond length
+------------------------------------------------------------------------- */
+
+double BondMM3::equilibrium_distance(int i)
+{
+ return r0[i];
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void BondMM3::write_restart(FILE *fp)
+{
+ fwrite(&k2[1],sizeof(double),atom->nbondtypes,fp);
+ fwrite(&r0[1],sizeof(double),atom->nbondtypes,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void BondMM3::read_restart(FILE *fp)
+{
+ allocate();
+
+ if (comm->me == 0) {
+ fread(&k2[1],sizeof(double),atom->nbondtypes,fp);
+ fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
+ }
+ MPI_Bcast(&k2[1],atom->nbondtypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
+
+ for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void BondMM3::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->nbondtypes; i++)
+ fprintf(fp,"%d %g %g\n",i,k2[i],r0[i]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double BondMM3::single(int type, double rsq, int i, int j, double &fforce)
+{
+ /*
+ E = K(r-r0)^2 [1-2.55*(r-r0)+(7/12)*2.55^(2)*(r-r0)^2]
+ with -2.55 in angstrom^(-1) and (7/12)*2.55^(2) in angstrom^(-2)
+ These prefactors are converted here to the correct units
+ */
+ double K3 = -2.55/force->angstrom;
+ double K4 = 7.0/12.0*2.55*2.55/force->angstrom/force->angstrom;
+ double r = sqrt(rsq);
+ double dr = r - r0[type];
+ double dr2 = dr*dr;
+ double de_bond = 2.0*k2[type]*dr*(1.0 + 1.5*K3*dr + 2.0*K4*dr2);
+ if (r > 0.0) fforce = -de_bond/r;
+ else fforce = 0.0;
+ return k2[type]*dr2*(1.0+K3*dr+K4*dr2);
+}
diff --git a/src/USER-YAFF/bond_mm3.h b/src/USER-YAFF/bond_mm3.h
new file mode 100644
index 0000000000000000000000000000000000000000..9711d895290e18aa40a4cfb6e35695673e176f44
--- /dev/null
+++ b/src/USER-YAFF/bond_mm3.h
@@ -0,0 +1,57 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef BOND_CLASS
+
+BondStyle(mm3,BondMM3)
+
+#else
+
+#ifndef LMP_BOND_MM3_H
+#define LMP_BOND_MM3_H
+
+#include <stdio.h>
+#include "bond.h"
+
+namespace LAMMPS_NS {
+
+class BondMM3 : public Bond {
+ public:
+ BondMM3(class LAMMPS *);
+ virtual ~BondMM3();
+ virtual void compute(int, int);
+ void coeff(int, char **);
+ double equilibrium_distance(int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ void write_data(FILE *);
+ double single(int, double, int, int, double &);
+
+ protected:
+ double *r0,*k2;
+
+ void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Incorrect args for bond coefficients
+
+Self-explanatory. Check the input script or data file.
+
+*/
diff --git a/src/USER-YAFF/improper_distharm.cpp b/src/USER-YAFF/improper_distharm.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..9a54afed9a473c0740693bb13cbe311b846215af
--- /dev/null
+++ b/src/USER-YAFF/improper_distharm.cpp
@@ -0,0 +1,269 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Steven Vandenbrande, heavily based on the
+ improper_distance code by Paolo Raiteri (Curtin University)
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include "improper_distharm.h"
+#include "atom.h"
+#include "comm.h"
+#include "neighbor.h"
+#include "domain.h"
+#include "force.h"
+#include "update.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define TOLERANCE 0.05
+#define SMALL 0.001
+
+/* ---------------------------------------------------------------------- */
+
+ImproperDistHarm::ImproperDistHarm(LAMMPS *lmp) : Improper(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+ImproperDistHarm::~ImproperDistHarm()
+{
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(k);
+ memory->destroy(chi);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ImproperDistHarm::compute(int eflag, int vflag)
+{
+ int i1,i2,i3,i4,n,type;
+ double xab, yab, zab; // bond 1-2
+ double xac, yac, zac; // bond 1-3
+ double xad, yad, zad; // bond 1-4
+ double xbc, ybc, zbc; // bond 2-3
+ double xbd, ybd, zbd; // bond 2-4
+ double xcd, ycd, zcd; // bond 3-4
+ double xna, yna, zna, rna; // normal
+ double da;
+
+ double eimproper,f1[3],f2[3],f3[3],f4[3];
+ double domega,a;
+
+ eimproper = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int **improperlist = neighbor->improperlist;
+ int nimproperlist = neighbor->nimproperlist;
+ int nlocal = atom->nlocal;
+ int newton_bond = force->newton_bond;
+
+ for (n = 0; n < nimproperlist; n++) {
+ i1 = improperlist[n][0];
+ i2 = improperlist[n][1];
+ i3 = improperlist[n][2];
+ i4 = improperlist[n][3];
+ type = improperlist[n][4];
+
+ // geometry of 4-body
+ // 4 is the central atom
+ // 1-2-3 are ment to be equivalent
+ // I need the bonds between 2-3 and 3-4 to get the plane normal
+ // Then I need the bond 1-4 to project it onto the normal to the plane
+
+ // bond 1->2
+ xab = x[i2][0] - x[i1][0];
+ yab = x[i2][1] - x[i1][1];
+ zab = x[i2][2] - x[i1][2];
+ domain->minimum_image(xab,yab,zab);
+
+ // bond 1->3
+ xac = x[i3][0] - x[i1][0];
+ yac = x[i3][1] - x[i1][1];
+ zac = x[i3][2] - x[i1][2];
+ domain->minimum_image(xac,yac,zac);
+
+ // bond 1->4
+ xad = x[i4][0] - x[i1][0];
+ yad = x[i4][1] - x[i1][1];
+ zad = x[i4][2] - x[i1][2];
+ domain->minimum_image(xad,yad,zad);
+
+ // bond 2-3
+ xbc = x[i3][0] - x[i2][0];
+ ybc = x[i3][1] - x[i2][1];
+ zbc = x[i3][2] - x[i2][2];
+ domain->minimum_image(xbc,ybc,zbc);
+
+ // bond 2-4
+ xbd = x[i4][0] - x[i2][0];
+ ybd = x[i4][1] - x[i2][1];
+ zbd = x[i4][2] - x[i2][2];
+ domain->minimum_image(xbd,ybd,zbd);
+
+ // bond 3-4
+ xcd = x[i4][0] - x[i3][0];
+ ycd = x[i4][1] - x[i3][1];
+ zcd = x[i4][2] - x[i3][2];
+ domain->minimum_image(xcd,ycd,zcd);
+
+ xna = ybc*zcd - zbc*ycd;
+ yna = -(xbc*zcd - zbc*xcd);
+ zna = xbc*ycd - ybc*xcd;
+ rna = 1.0 / sqrt(xna*xna+yna*yna+zna*zna);
+ xna *= rna;
+ yna *= rna;
+ zna *= rna;
+
+ da = -(xna*xad + yna*yad + zna*zad);
+
+
+ domega = k[type]*(da - chi[type])*(da - chi[type]);
+ a = 2.0* k[type]*(da - chi[type]);
+
+ if (eflag) eimproper = domega;
+
+ f1[0] = a*( -xna);
+ f1[1] = a*( -yna);
+ f1[2] = a*( -zna);
+ f4[0] = a*( xna);
+ f4[1] = a*( yna);
+ f4[2] = a*( zna);
+
+ f2[0] = a*( yad*zcd - zad*ycd )*rna + a*da*rna*( yna*zcd - zna*ycd);
+ f2[1] = a*( zad*xcd - xad*zcd )*rna + a*da*rna*( zna*xcd - xna*zcd);
+ f2[2] = a*( xad*ycd - yad*xcd )*rna + a*da*rna*( xna*ycd - yna*xcd);
+
+ f3[0] = - a*( yad*zcd - zad*ycd )*rna - a*da*rna*( yna*zcd - zna*ycd);
+ f3[1] = - a*( zad*xcd - xad*zcd )*rna - a*da*rna*( zna*xcd - xna*zcd);
+ f3[2] = - a*( xad*ycd - yad*xcd )*rna - a*da*rna*( xna*ycd - yna*xcd);
+
+ f3[0] += -a*( yad*zbc - zad*ybc )*rna - a*da*rna*( yna*zbc - zna*ybc);
+ f3[1] += -a*( zad*xbc - xad*zbc )*rna - a*da*rna*( zna*xbc - xna*zbc);
+ f3[2] += -a*( xad*ybc - yad*xbc )*rna - a*da*rna*( xna*ybc - yna*xbc);
+ f4[0] += a*( yad*zbc - zad*ybc )*rna + a*da*rna*( yna*zbc - zna*ybc);
+ f4[1] += a*( zad*xbc - xad*zbc )*rna + a*da*rna*( zna*xbc - xna*zbc);
+ f4[2] += a*( xad*ybc - yad*xbc )*rna + a*da*rna*( xna*ybc - yna*xbc);
+
+ // apply force to each of 4 atoms
+
+ if (newton_bond || i1 < nlocal) {
+ f[i1][0] += f1[0];
+ f[i1][1] += f1[1];
+ f[i1][2] += f1[2];
+ }
+
+ if (newton_bond || i2 < nlocal) {
+ f[i2][0] += f2[0];
+ f[i2][1] += f2[1];
+ f[i2][2] += f2[2];
+ }
+
+ if (newton_bond || i3 < nlocal) {
+ f[i3][0] += f3[0];
+ f[i3][1] += f3[1];
+ f[i3][2] += f3[2];
+ }
+
+ if (newton_bond || i4 < nlocal) {
+ f[i4][0] += f4[0];
+ f[i4][1] += f4[1];
+ f[i4][2] += f4[2];
+ }
+
+ if (evflag)
+ ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f2,f3,f4,
+ xab,yab,zab,xac,yac,zac,xad-xac,yad-yac,zad-zac);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ImproperDistHarm::allocate()
+{
+ allocated = 1;
+ int n = atom->nimpropertypes;
+
+ memory->create(k,n+1,"improper:k");
+ memory->create(chi,n+1,"improper:chi");
+
+ memory->create(setflag,n+1,"improper:setflag");
+ for (int i = 1; i <= n; i++) setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one type
+------------------------------------------------------------------------- */
+
+void ImproperDistHarm::coeff(int narg, char **arg)
+{
+// if (which > 0) return;
+ if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi;
+ force->bounds(FLERR,arg[0],atom->nimpropertypes,ilo,ihi);
+
+ double k_one = force->numeric(FLERR,arg[1]);
+ double chi_one = force->numeric(FLERR,arg[2]);
+
+ // convert chi from degrees to radians
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ k[i] = k_one;
+ //chi[i] = chi_one/180.0 * PI;
+ chi[i] = chi_one;
+ setflag[i] = 1;
+ count++;
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void ImproperDistHarm::write_restart(FILE *fp)
+{
+ fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
+ fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void ImproperDistHarm::read_restart(FILE *fp)
+{
+ allocate();
+
+ if (comm->me == 0) {
+ fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
+ fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
+ }
+ MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
+
+ for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
+}
diff --git a/src/USER-YAFF/improper_distharm.h b/src/USER-YAFF/improper_distharm.h
new file mode 100644
index 0000000000000000000000000000000000000000..b8b9ae780e06d592f10a0e7b27926b4ce916a5b6
--- /dev/null
+++ b/src/USER-YAFF/improper_distharm.h
@@ -0,0 +1,47 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef IMPROPER_CLASS
+
+ImproperStyle(distharm,ImproperDistHarm)
+
+#else
+
+#ifndef LMP_IMPROPER_DISTHARM_H
+#define LMP_IMPROPER_DISTHARM_H
+
+#include <stdio.h>
+#include "improper.h"
+
+namespace LAMMPS_NS {
+
+class ImproperDistHarm : public Improper {
+ public:
+ ImproperDistHarm(class LAMMPS *);
+ ~ImproperDistHarm();
+ void compute(int, int);
+ void coeff(int, char **);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+
+ private:
+ double *k,*chi;
+
+ void allocate();
+};
+
+}
+
+#endif
+#endif
+
diff --git a/src/USER-YAFF/improper_sqdistharm.cpp b/src/USER-YAFF/improper_sqdistharm.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..763d82f1c55faa5f84f50b4cf4755ab5eb2bb08f
--- /dev/null
+++ b/src/USER-YAFF/improper_sqdistharm.cpp
@@ -0,0 +1,269 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Steven Vandenbrande, heavily based on the
+ improper_distance code by Paolo Raiteri (Curtin University)
+------------------------------------------------------------------------- */
+
+#include <mpi.h>
+#include <math.h>
+#include <stdlib.h>
+#include "improper_sqdistharm.h"
+#include "atom.h"
+#include "comm.h"
+#include "neighbor.h"
+#include "domain.h"
+#include "force.h"
+#include "update.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+#define TOLERANCE 0.05
+#define SMALL 0.001
+
+/* ---------------------------------------------------------------------- */
+
+ImproperSQDistHarm::ImproperSQDistHarm(LAMMPS *lmp) : Improper(lmp) {}
+
+/* ---------------------------------------------------------------------- */
+
+ImproperSQDistHarm::~ImproperSQDistHarm()
+{
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(k);
+ memory->destroy(chi);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ImproperSQDistHarm::compute(int eflag, int vflag)
+{
+ int i1,i2,i3,i4,n,type;
+ double xab, yab, zab; // bond 1-2
+ double xac, yac, zac; // bond 1-3
+ double xad, yad, zad; // bond 1-4
+ double xbc, ybc, zbc; // bond 2-3
+ double xbd, ybd, zbd; // bond 2-4
+ double xcd, ycd, zcd; // bond 3-4
+ double xna, yna, zna, rna; // normal
+ double da;
+
+ double eimproper,f1[3],f2[3],f3[3],f4[3];
+ double domega,a;
+
+ eimproper = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ int **improperlist = neighbor->improperlist;
+ int nimproperlist = neighbor->nimproperlist;
+ int nlocal = atom->nlocal;
+ int newton_bond = force->newton_bond;
+
+ for (n = 0; n < nimproperlist; n++) {
+ i1 = improperlist[n][0];
+ i2 = improperlist[n][1];
+ i3 = improperlist[n][2];
+ i4 = improperlist[n][3];
+ type = improperlist[n][4];
+
+ // geometry of 4-body
+ // 4 is the central atom
+ // 1-2-3 are ment to be equivalent
+ // I need the bonds between 2-3 and 3-4 to get the plane normal
+ // Then I need the bond 1-4 to project it onto the normal to the plane
+
+ // bond 1->2
+ xab = x[i2][0] - x[i1][0];
+ yab = x[i2][1] - x[i1][1];
+ zab = x[i2][2] - x[i1][2];
+ domain->minimum_image(xab,yab,zab);
+
+ // bond 1->3
+ xac = x[i3][0] - x[i1][0];
+ yac = x[i3][1] - x[i1][1];
+ zac = x[i3][2] - x[i1][2];
+ domain->minimum_image(xac,yac,zac);
+
+ // bond 1->4
+ xad = x[i4][0] - x[i1][0];
+ yad = x[i4][1] - x[i1][1];
+ zad = x[i4][2] - x[i1][2];
+ domain->minimum_image(xad,yad,zad);
+
+ // bond 2-3
+ xbc = x[i3][0] - x[i2][0];
+ ybc = x[i3][1] - x[i2][1];
+ zbc = x[i3][2] - x[i2][2];
+ domain->minimum_image(xbc,ybc,zbc);
+
+ // bond 2-4
+ xbd = x[i4][0] - x[i2][0];
+ ybd = x[i4][1] - x[i2][1];
+ zbd = x[i4][2] - x[i2][2];
+ domain->minimum_image(xbd,ybd,zbd);
+
+ // bond 3-4
+ xcd = x[i4][0] - x[i3][0];
+ ycd = x[i4][1] - x[i3][1];
+ zcd = x[i4][2] - x[i3][2];
+ domain->minimum_image(xcd,ycd,zcd);
+
+ xna = ybc*zcd - zbc*ycd;
+ yna = -(xbc*zcd - zbc*xcd);
+ zna = xbc*ycd - ybc*xcd;
+ rna = 1.0 / sqrt(xna*xna+yna*yna+zna*zna);
+ xna *= rna;
+ yna *= rna;
+ zna *= rna;
+
+ da = -(xna*xad + yna*yad + zna*zad);
+
+ domega = k[type]*(da*da - chi[type])*(da*da - chi[type]);
+ a = 4.0 * da* k[type]*(da*da - chi[type]);
+
+ if (eflag) eimproper = domega;
+
+ f1[0] = a*( -xna);
+ f1[1] = a*( -yna);
+ f1[2] = a*( -zna);
+ f4[0] = a*( xna);
+ f4[1] = a*( yna);
+ f4[2] = a*( zna);
+
+ f2[0] = a*( yad*zcd - zad*ycd )*rna + a*da*rna*( yna*zcd - zna*ycd);
+ f2[1] = a*( zad*xcd - xad*zcd )*rna + a*da*rna*( zna*xcd - xna*zcd);
+ f2[2] = a*( xad*ycd - yad*xcd )*rna + a*da*rna*( xna*ycd - yna*xcd);
+
+ f3[0] = - a*( yad*zcd - zad*ycd )*rna - a*da*rna*( yna*zcd - zna*ycd);
+ f3[1] = - a*( zad*xcd - xad*zcd )*rna - a*da*rna*( zna*xcd - xna*zcd);
+ f3[2] = - a*( xad*ycd - yad*xcd )*rna - a*da*rna*( xna*ycd - yna*xcd);
+
+ f3[0] += -a*( yad*zbc - zad*ybc )*rna - a*da*rna*( yna*zbc - zna*ybc);
+ f3[1] += -a*( zad*xbc - xad*zbc )*rna - a*da*rna*( zna*xbc - xna*zbc);
+ f3[2] += -a*( xad*ybc - yad*xbc )*rna - a*da*rna*( xna*ybc - yna*xbc);
+ f4[0] += a*( yad*zbc - zad*ybc )*rna + a*da*rna*( yna*zbc - zna*ybc);
+ f4[1] += a*( zad*xbc - xad*zbc )*rna + a*da*rna*( zna*xbc - xna*zbc);
+ f4[2] += a*( xad*ybc - yad*xbc )*rna + a*da*rna*( xna*ybc - yna*xbc);
+
+
+ // apply force to each of 4 atoms
+
+ if (newton_bond || i1 < nlocal) {
+ f[i1][0] += f1[0];
+ f[i1][1] += f1[1];
+ f[i1][2] += f1[2];
+ }
+
+ if (newton_bond || i2 < nlocal) {
+ f[i2][0] += f2[0];
+ f[i2][1] += f2[1];
+ f[i2][2] += f2[2];
+ }
+
+ if (newton_bond || i3 < nlocal) {
+ f[i3][0] += f3[0];
+ f[i3][1] += f3[1];
+ f[i3][2] += f3[2];
+ }
+
+ if (newton_bond || i4 < nlocal) {
+ f[i4][0] += f4[0];
+ f[i4][1] += f4[1];
+ f[i4][2] += f4[2];
+ }
+
+ if (evflag)
+ ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f2,f3,f4,
+ xab,yab,zab,xac,yac,zac,xad-xac,yad-yac,zad-zac);
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ImproperSQDistHarm::allocate()
+{
+ allocated = 1;
+ int n = atom->nimpropertypes;
+
+ memory->create(k,n+1,"improper:k");
+ memory->create(chi,n+1,"improper:chi");
+
+ memory->create(setflag,n+1,"improper:setflag");
+ for (int i = 1; i <= n; i++) setflag[i] = 0;
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one type
+------------------------------------------------------------------------- */
+
+void ImproperSQDistHarm::coeff(int narg, char **arg)
+{
+// if (which > 0) return;
+ if (narg != 3) error->all(FLERR,"Incorrect args for improper coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi;
+ force->bounds(FLERR,arg[0],atom->nimpropertypes,ilo,ihi);
+
+ double k_one = force->numeric(FLERR,arg[1]);
+ double chi_one = force->numeric(FLERR,arg[2]);
+
+ // convert chi from degrees to radians
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ k[i] = k_one;
+ //chi[i] = chi_one/180.0 * PI;
+ chi[i] = chi_one;
+ setflag[i] = 1;
+ count++;
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for improper coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes out coeffs to restart file
+------------------------------------------------------------------------- */
+
+void ImproperSQDistHarm::write_restart(FILE *fp)
+{
+ fwrite(&k[1],sizeof(double),atom->nimpropertypes,fp);
+ fwrite(&chi[1],sizeof(double),atom->nimpropertypes,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads coeffs from restart file, bcasts them
+------------------------------------------------------------------------- */
+
+void ImproperSQDistHarm::read_restart(FILE *fp)
+{
+ allocate();
+
+ if (comm->me == 0) {
+ fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
+ fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
+ }
+ MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
+ MPI_Bcast(&chi[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
+
+ for (int i = 1; i <= atom->nimpropertypes; i++) setflag[i] = 1;
+}
diff --git a/src/USER-YAFF/improper_sqdistharm.h b/src/USER-YAFF/improper_sqdistharm.h
new file mode 100644
index 0000000000000000000000000000000000000000..301b5066cbabc4d8a877dd0b56caf603634ac450
--- /dev/null
+++ b/src/USER-YAFF/improper_sqdistharm.h
@@ -0,0 +1,47 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef IMPROPER_CLASS
+
+ImproperStyle(sqdistharm,ImproperSQDistHarm)
+
+#else
+
+#ifndef LMP_IMPROPER_SQDISTHARM_H
+#define LMP_IMPROPER_SQDISTHARM_H
+
+#include <stdio.h>
+#include "improper.h"
+
+namespace LAMMPS_NS {
+
+class ImproperSQDistHarm : public Improper {
+ public:
+ ImproperSQDistHarm(class LAMMPS *);
+ ~ImproperSQDistHarm();
+ void compute(int, int);
+ void coeff(int, char **);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+
+ private:
+ double *k,*chi;
+
+ void allocate();
+};
+
+}
+
+#endif
+#endif
+
diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..b3a267807dbc9c1465ce3ebd726377ce62fc18c0
--- /dev/null
+++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.cpp
@@ -0,0 +1,714 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Steven Vandenbrande
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "pair_lj_switch3_coulgauss_long.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "kspace.h"
+#include "update.h"
+#include "integrate.h"
+#include "respa.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define EWALD_F 1.12837917
+#define EWALD_P 0.3275911
+#define A1 0.254829592
+#define A2 -0.284496736
+#define A3 1.421413741
+#define A4 -1.453152027
+#define A5 1.061405429
+
+/* ---------------------------------------------------------------------- */
+
+PairLJSwitch3CoulGaussLong::PairLJSwitch3CoulGaussLong(LAMMPS *lmp) : Pair(lmp)
+{
+ ewaldflag = pppmflag = 1;
+ respa_enable = 1;
+ writedata = 1;
+ ftable = NULL;
+ qdist = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairLJSwitch3CoulGaussLong::~PairLJSwitch3CoulGaussLong()
+{
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(cut_lj);
+ memory->destroy(cut_ljsq);
+ memory->destroy(epsilon);
+ memory->destroy(sigma);
+ memory->destroy(gamma);
+ memory->destroy(lj1);
+ memory->destroy(lj2);
+ memory->destroy(lj3);
+ memory->destroy(lj4);
+ memory->destroy(offset);
+ }
+ if (ftable) free_tables();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairLJSwitch3CoulGaussLong::compute(int eflag, int vflag)
+{
+ int i,ii,j,jj,inum,jnum,itype,jtype,itable,jtable,ktable;
+ double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,ecoul2,fpair;
+ double fraction,fraction2,table;
+ double r,r2inv,r6inv,forcecoul,forcecoul2,forcelj,factor_coul,factor_lj,tr,ftr,trx;
+ double grij,expm2,prefactor,prefactor2,t,erfc1,erfc2,rrij,expn2,expb,g_ewald2i,g_ewaldi;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ double rsq, lookup_corr;
+
+ evdwl = ecoul = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ double *q = atom->q;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ double *special_coul = force->special_coul;
+ double *special_lj = force->special_lj;
+ int newton_pair = force->newton_pair;
+ double qqrd2e = force->qqrd2e;
+ union_int_float_t rsq_lookup;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+ g_ewaldi = 1.0/g_ewald;
+ g_ewald2i = g_ewaldi*g_ewaldi;
+ lookup_corr = 0.0;
+
+ // loop over neighbors of my atoms
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ qtmp = q[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ factor_coul = special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+
+ if (rsq < cutsq[itype][jtype]) {
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc1 = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc1 + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ // Lennard-Jones potential
+ r = sqrt(rsq);
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj = r6inv*(12.0*lj3[itype][jtype]*r6inv - 6.0*lj4[itype][jtype]);
+ // Correction for Gaussian radii
+ if (lj2[itype][jtype]==0.0) {
+ // This means a point charge is considerd, so the correction is zero
+ expn2 = 0.0;
+ erfc2 = 0.0;
+ forcecoul2 = 0.0;
+ }
+ else {
+ rrij = lj2[itype][jtype]*r;
+ expn2 = exp(-rrij*rrij);
+ erfc2 = erfc(rrij);
+ prefactor2 = -qqrd2e*qtmp*q[j]/r;
+ forcecoul2 = prefactor2*(erfc2+EWALD_F*rrij*expn2);
+ }
+ } else forcelj = 0.0;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc1;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ ecoul += prefactor2*erfc2*factor_coul;
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ } else evdwl = 0.0;
+
+ // Truncation, see Yaff Switch33
+ if (truncw>0) {
+ if (rsq < cut_ljsq[itype][jtype]) {
+ if (r>cut_lj[itype][jtype]-truncw) {
+ trx = (cut_lj[itype][jtype]-r)*truncwi;
+ tr = trx*trx*(3.0-2.0*trx);
+ ftr = 6.0*trx*(1.0-trx)*r*truncwi;
+ forcelj = forcelj*tr + evdwl*ftr;
+ evdwl *= tr;
+ }
+ }
+ }
+
+ fpair = (forcecoul + factor_coul*forcecoul2 + factor_lj*forcelj) * r2inv;
+ evdwl *= factor_lj;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairLJSwitch3CoulGaussLong::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+ memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
+ memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
+ memory->create(epsilon,n+1,n+1,"pair:epsilon");
+ memory->create(sigma,n+1,n+1,"pair:sigma");
+ memory->create(gamma,n+1,n+1,"pair:gamma");
+ memory->create(lj1,n+1,n+1,"pair:lj1");
+ memory->create(lj2,n+1,n+1,"pair:lj2");
+ memory->create(lj3,n+1,n+1,"pair:lj3");
+ memory->create(lj4,n+1,n+1,"pair:lj4");
+ memory->create(offset,n+1,n+1,"pair:offset");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+void PairLJSwitch3CoulGaussLong::settings(int narg, char **arg)
+{
+ if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
+
+ cut_lj_global = force->numeric(FLERR,arg[0]);
+ if (narg == 2) {
+ cut_coul = cut_lj_global;
+ truncw = force->numeric(FLERR,arg[1]);
+ }
+ else {
+ cut_coul = force->numeric(FLERR,arg[1]);
+ truncw = force->numeric(FLERR,arg[2]);
+ }
+ if (truncw>0.0) truncwi = 1.0/truncw;
+ else truncwi = 0.0;
+ // reset cutoffs that have been explicitly set
+
+ if (allocated) {
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++)
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairLJSwitch3CoulGaussLong::coeff(int narg, char **arg)
+{
+ if (narg < 5 || narg > 6)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi,jlo,jhi;
+ force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+ force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+
+ double epsilon_one = force->numeric(FLERR,arg[2]);
+ double sigma_one = force->numeric(FLERR,arg[3]);
+ double gamma_one = force->numeric(FLERR,arg[4]);
+
+ double cut_lj_one = cut_lj_global;
+ if (narg == 6) cut_lj_one = force->numeric(FLERR,arg[5]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ epsilon[i][j] = epsilon_one;
+ sigma[i][j] = sigma_one;
+ gamma[i][j] = gamma_one;
+ cut_lj[i][j] = cut_lj_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairLJSwitch3CoulGaussLong::init_style()
+{
+ if (!atom->q_flag)
+ error->all(FLERR,"Pair style lj/switch3/coulgauss/long requires atom attribute q");
+
+ // request regular or rRESPA neighbor list
+
+ int irequest;
+ int respa = 0;
+
+ if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
+ if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
+ if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
+ }
+
+ irequest = neighbor->request(this,instance_me);
+
+ if (respa >= 1) {
+ neighbor->requests[irequest]->respaouter = 1;
+ neighbor->requests[irequest]->respainner = 1;
+ }
+ if (respa == 2) neighbor->requests[irequest]->respamiddle = 1;
+
+ cut_coulsq = cut_coul * cut_coul;
+
+ // set rRESPA cutoffs
+
+ if (strstr(update->integrate_style,"respa") &&
+ ((Respa *) update->integrate)->level_inner >= 0)
+ cut_respa = ((Respa *) update->integrate)->cutoff;
+ else cut_respa = NULL;
+
+ // insure use of KSpace long-range solver, set g_ewald
+
+ if (force->kspace == NULL)
+ error->all(FLERR,"Pair style requires a KSpace style");
+ g_ewald = force->kspace->g_ewald;
+
+ // setup force tables
+
+ if (ncoultablebits) init_tables(cut_coul,cut_respa);
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairLJSwitch3CoulGaussLong::init_one(int i, int j)
+{
+ if (setflag[i][j] == 0) {
+ epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
+ sigma[i][i],sigma[j][j]);
+ sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
+ gamma[i][j] = 1.0/sqrt(gamma[i][i]*gamma[i][i]+gamma[j][j]*gamma[j][j]);
+ cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
+ }
+
+ double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist);
+ cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
+ lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
+ if (gamma[i][i]==0.0 && gamma[j][j]==0.0) lj2[i][j] = 0.0;
+ else lj2[i][j] = 1.0/sqrt(gamma[i][i]*gamma[i][i]+gamma[j][j]*gamma[j][j]);
+ lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
+ lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
+
+ if (offset_flag && (cut_lj[i][j] > 0.0)) {
+ // Truncation is active, so offset is zero, except if truncw==0.0
+ if (truncw==0.0) {
+ double r = cut_lj[i][j];
+ double r2inv = 1.0/(r*r);
+ double r6inv = r2inv*r2inv*r2inv;
+ double r12inv = r6inv*r6inv;
+ offset[i][j] = lj3[i][j]*r12inv-lj4[i][j]*r6inv;
+ }
+ else {offset[i][j] = 0.0;}
+ } else offset[i][j] = 0.0;
+
+ cut_ljsq[j][i] = cut_ljsq[i][j];
+ cut_lj[j][i] = cut_lj[i][j];
+ lj1[j][i] = lj1[i][j];
+ lj2[j][i] = lj2[i][j];
+ lj3[j][i] = lj3[i][j];
+ lj4[j][i] = lj4[i][j];
+ offset[j][i] = offset[i][j];
+
+ // check interior rRESPA cutoff
+
+ if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3])
+ error->all(FLERR,"Pair cutoff < Respa interior cutoff");
+
+ // compute I,J contribution to long-range tail correction
+ // count total # of atoms of type I and J via Allreduce
+
+ if (tail_flag) {
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+
+ double count[2],all[2];
+ count[0] = count[1] = 0.0;
+ for (int k = 0; k < nlocal; k++) {
+ if (type[k] == i) count[0] += 1.0;
+ if (type[k] == j) count[1] += 1.0;
+ }
+ MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
+
+ double cg = epsilon[i][j];
+ double cg1 = cut_lj[i][j];
+ double cg3 = sigma[i][j];
+ if (truncw > 0.0) {
+ double cg5 = truncw;
+ double t1 = pow(cg1, 0.2e1);
+ double t2 = t1 * cg1;
+ double t3 = t1 * t1;
+ double t4 = t3 * t2;
+ double t5 = -cg1 + cg5;
+ double t6 = t5 * t5;
+ double t8 = t6 * t6;
+ double t9 = t8 * t6 * t5;
+ double t10 = t4 * t9;
+ double t11 = log(-t5);
+ double t14 = log(cg1);
+ double t19 = pow(cg5, 0.2e1);
+ double t20 = t19 * t19;
+ double t21 = t20 * t19;
+ double t24 = pow(cg3, 0.2e1);
+ double t25 = t24 * t24;
+ double t26 = t25 * t24;
+ double t29 = t20 * cg5;
+ double t35 = t3 * t3;
+ double t41 = t19 * cg5;
+ double t58 = t21 * t3 * t1 - t21 * t26 / 0.84e2 - 0.6e1 * t29 * t4 + t29 * cg1 * t26 / 0.18e2 + 0.15e2 * t20 * t35 - t20 * t1 * t26 / 0.9e1 - 0.20e2 * t41 * t35 * cg1 + t41 * t2 * t26 / 0.9e1 + 0.15e2 * t19 * t35 * t1 - t19 * t3 * t26 / 0.18e2 - 0.6e1 * t35 * t2 * cg5 + t35 * t3;
+ double t71 = -0.4e1 * cg * (0.2e1 * t10 * t11 - 0.2e1 * t10 * t14 + (cg5 - 0.2e1 * cg1) * t58 * cg5) * t26 / t4 / t41 / t9;
+ etail_ij = 2.0*MY_PI*all[0]*all[1]*t71;
+ ptail_ij = 2.0*MY_PI*all[0]*all[1]*t71;
+ }
+ else {
+ double t1 = pow(cg3, 0.2e1);
+ double t2 = t1 * t1;
+ double t3 = t2 * t1;
+ double t5 = pow(cg1, 0.2e1);
+ double t6 = t5 * t5;
+ double t10 = t6 * t6;
+ double t16 = -0.4e1 / 0.9e1 * t3 * cg * (0.3e1 * t6 * t5 - t3) / t10 / cg1;
+ t1 = pow(cg3, 0.2e1);
+ t2 = t1 * t1;
+ t3 = t2 * t1;
+ t5 = pow(cg1, 0.2e1);
+ t6 = t5 * t5;
+ double t11 = t6 * t6;
+ double t17 = 0.8e1 / 0.3e1 * t3 * cg * (0.3e1 * t6 * t5 - 0.2e1 * t3) / t11 / cg1;
+ etail_ij = 2.0*MY_PI*all[0]*all[1]*t16;
+ ptail_ij = -2.0/3.0*MY_PI*all[0]*all[1]*t17;
+ }
+ }
+
+ return cut;
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLJSwitch3CoulGaussLong::write_restart(FILE *fp)
+{
+ write_restart_settings(fp);
+
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ fwrite(&setflag[i][j],sizeof(int),1,fp);
+ if (setflag[i][j]) {
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&gamma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLJSwitch3CoulGaussLong::read_restart(FILE *fp)
+{
+ read_restart_settings(fp);
+
+ allocate();
+
+ int i,j;
+ int me = comm->me;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+ MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+ if (setflag[i][j]) {
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&gamma[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairLJSwitch3CoulGaussLong::write_restart_settings(FILE *fp)
+{
+ fwrite(&cut_lj_global,sizeof(double),1,fp);
+ fwrite(&cut_coul,sizeof(double),1,fp);
+ fwrite(&truncw,sizeof(double),1,fp);
+ fwrite(&offset_flag,sizeof(int),1,fp);
+ fwrite(&mix_flag,sizeof(int),1,fp);
+ fwrite(&tail_flag,sizeof(int),1,fp);
+ fwrite(&ncoultablebits,sizeof(int),1,fp);
+ fwrite(&tabinner,sizeof(double),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairLJSwitch3CoulGaussLong::read_restart_settings(FILE *fp)
+{
+ if (comm->me == 0) {
+ fread(&cut_lj_global,sizeof(double),1,fp);
+ fread(&cut_coul,sizeof(double),1,fp);
+ fread(&truncw,sizeof(double),1,fp);
+ fread(&offset_flag,sizeof(int),1,fp);
+ fread(&mix_flag,sizeof(int),1,fp);
+ fread(&tail_flag,sizeof(int),1,fp);
+ fread(&ncoultablebits,sizeof(int),1,fp);
+ fread(&tabinner,sizeof(double),1,fp);
+ }
+ MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&truncw,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
+ MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
+}
+
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairLJSwitch3CoulGaussLong::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],gamma[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairLJSwitch3CoulGaussLong::write_data_all(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ for (int j = i; j <= atom->ntypes; j++)
+ fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],gamma[i][j],cut_lj[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairLJSwitch3CoulGaussLong::single(int i, int j, int itype, int jtype,
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
+{
+ double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2,rrij,expn2,erfc2;
+ double fraction,table,forcecoul,forcecoul2,forcelj,phicoul,phicoul2,philj;
+ double expb, ecoul, evdwl, trx, tr, ftr;
+
+ int itable;
+
+ r2inv = 1.0/rsq;
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc1 = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
+ forcecoul = prefactor * (erfc1 + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup_single;
+ rsq_lookup_single.f = rsq;
+ itable = rsq_lookup_single.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup_single.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = atom->q[i]*atom->q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = atom->q[i]*atom->q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r = sqrt(rsq);
+ r6inv = r2inv*r2inv*r2inv;
+ rrij = lj2[itype][jtype] * r;
+ if (rrij==0.0) {
+ expn2 = 0.0;
+ erfc2 = 0.0;
+ }
+ else {
+ expn2 = exp(-rrij*rrij);
+ erfc2 = erfc(rrij);
+ }
+ prefactor2 = -force->qqrd2e * atom->q[i]*atom->q[j]/r;
+ forcecoul2 = prefactor2 * (erfc2 + EWALD_F*rrij*expn2);
+ forcelj = expb*lj1[itype][jtype]*r-6.0*lj4[itype][jtype]*r6inv;
+ } else forcelj = 0.0;
+
+ double eng = 0.0;
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ phicoul = prefactor*erfc1;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ phicoul = atom->q[i]*atom->q[j] * table;
+ }
+ if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
+ eng += phicoul;
+ }
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ ecoul += prefactor2*erfc2*factor_coul;
+ evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
+ offset[itype][jtype];
+ } else evdwl = 0.0;
+
+ // Truncation, see Yaff Switch3
+ if (truncw>0) {
+ if (rsq < cut_ljsq[itype][jtype]) {
+ if (r>cut_lj[itype][jtype]-truncw) {
+ trx = (cut_lj[itype][jtype]-r)*truncwi;
+ tr = trx*trx*(3.0-2.0*trx);
+ ftr = 6.0*trx*(1.0-trx)*r*truncwi;
+ forcelj = forcelj*tr + evdwl*ftr;
+ evdwl *= tr;
+ }
+ }
+ }
+ eng += evdwl*factor_lj;
+ fforce = (forcecoul + factor_coul*forcecoul2 + factor_lj*forcelj) * r2inv;
+
+ return eng;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairLJSwitch3CoulGaussLong::extract(const char *str, int &dim)
+{
+ dim = 0;
+ if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
+ dim = 2;
+ if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
+ if (strcmp(str,"sigma") == 0) return (void *) sigma;
+ if (strcmp(str,"gamma") == 0) return (void *) gamma;
+ return NULL;
+}
diff --git a/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h
new file mode 100644
index 0000000000000000000000000000000000000000..75686d55a2cb1932874eb65014ff4d2af4ff2287
--- /dev/null
+++ b/src/USER-YAFF/pair_lj_switch3_coulgauss_long.h
@@ -0,0 +1,91 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(lj/switch3/coulgauss/long,PairLJSwitch3CoulGaussLong)
+
+#else
+
+#ifndef LMP_PAIR_LJ_SWITCH3_COULGAUSS_LONG_H
+#define LMP_PAIR_LJ_SWITCH3_COULGAUSS_LONG_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairLJSwitch3CoulGaussLong : public Pair {
+
+ public:
+ PairLJSwitch3CoulGaussLong(class LAMMPS *);
+ virtual ~PairLJSwitch3CoulGaussLong();
+ virtual void compute(int, int);
+ virtual void settings(int, char **);
+ void coeff(int, char **);
+ virtual void init_style();
+ virtual double init_one(int, int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ virtual void write_restart_settings(FILE *);
+ virtual void read_restart_settings(FILE *);
+ void write_data(FILE *);
+ void write_data_all(FILE *);
+ virtual double single(int, int, int, int, double, double, double, double &);
+
+ virtual void *extract(const char *, int &);
+
+ protected:
+ double cut_lj_global;
+ double truncw, truncwi;
+ double **cut_lj,**cut_ljsq;
+ double cut_coul,cut_coulsq;
+ double **epsilon,**sigma,**gamma;
+ double **lj1,**lj2,**lj3,**lj4,**offset;
+ double *cut_respa;
+ double qdist; // TIP4P distance from O site to negative charge
+ double g_ewald;
+
+ virtual void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory. Check the input script or data file.
+
+E: Pair style lj/switch3/coulgauss/long requires atom attribute q
+
+The atom style defined does not have this attribute.
+
+E: Pair style requires a KSpace style
+
+No kspace style is defined.
+
+E: Pair cutoff < Respa interior cutoff
+
+One or more pairwise cutoffs are too short to use with the specified
+rRESPA cutoffs.
+
+*/
diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..0d0e43a0ea00533ff09b02f0f5b7d91fc8dc84e8
--- /dev/null
+++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.cpp
@@ -0,0 +1,715 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Steven Vandenbrande
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "pair_mm3_switch3_coulgauss_long.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "kspace.h"
+#include "update.h"
+#include "integrate.h"
+#include "respa.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define EWALD_F 1.12837917
+#define EWALD_P 0.3275911
+#define A1 0.254829592
+#define A2 -0.284496736
+#define A3 1.421413741
+#define A4 -1.453152027
+#define A5 1.061405429
+
+/* ---------------------------------------------------------------------- */
+
+PairMM3Switch3CoulGaussLong::PairMM3Switch3CoulGaussLong(LAMMPS *lmp) : Pair(lmp)
+{
+ ewaldflag = pppmflag = 1;
+ respa_enable = 1;
+ writedata = 1;
+ ftable = NULL;
+ qdist = 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PairMM3Switch3CoulGaussLong::~PairMM3Switch3CoulGaussLong()
+{
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+
+ memory->destroy(cut_lj);
+ memory->destroy(cut_ljsq);
+ memory->destroy(epsilon);
+ memory->destroy(sigma);
+ memory->destroy(gamma);
+ memory->destroy(lj1);
+ memory->destroy(lj2);
+ memory->destroy(lj3);
+ memory->destroy(lj4);
+ memory->destroy(offset);
+ }
+ if (ftable) free_tables();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairMM3Switch3CoulGaussLong::compute(int eflag, int vflag)
+{
+ int i,ii,j,jj,inum,jnum,itype,jtype,itable,jtable,ktable;
+ double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,ecoul2,fpair;
+ double fraction,fraction2,table;
+ double r,r2inv,r6inv,forcecoul,forcecoul2,forcelj,factor_coul,factor_lj,tr,ftr,trx;
+ double grij,expm2,prefactor,prefactor2,t,erfc1,erfc2,rrij,expn2,expb,g_ewald2i,g_ewaldi;
+ int *ilist,*jlist,*numneigh,**firstneigh;
+ double rsq, lookup_corr;
+
+ evdwl = ecoul = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ double *q = atom->q;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ double *special_coul = force->special_coul;
+ double *special_lj = force->special_lj;
+ int newton_pair = force->newton_pair;
+ double qqrd2e = force->qqrd2e;
+ union_int_float_t rsq_lookup;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+ g_ewaldi = 1.0/g_ewald;
+ g_ewald2i = g_ewaldi*g_ewaldi;
+ lookup_corr = 0.0;
+
+ // loop over neighbors of my atoms
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ qtmp = q[i];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ itype = type[i];
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ factor_lj = special_lj[sbmask(j)];
+ factor_coul = special_coul[sbmask(j)];
+ j &= NEIGHMASK;
+
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ rsq = delx*delx + dely*dely + delz*delz;
+ jtype = type[j];
+
+ if (rsq < cutsq[itype][jtype]) {
+ r2inv = 1.0/rsq;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc1 = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = qqrd2e * qtmp*q[j]/r;
+ forcecoul = prefactor * (erfc1 + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ rsq_lookup.f = rsq;
+ itable = rsq_lookup.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = qtmp*q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = qtmp*q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ // Repulsive exponential part
+ r = sqrt(rsq);
+ expb = lj3[itype][jtype]*exp(-lj1[itype][jtype]*r);
+ forcelj = expb*lj1[itype][jtype]*r;
+ // Attractive r^-6 part
+ r6inv = r2inv*r2inv*r2inv;
+ forcelj -= 6.0*lj4[itype][jtype]*r6inv;
+ // Correction for Gaussian radii
+ if (lj2[itype][jtype]==0.0) {
+ // This means a point charge is considered, so the correction is zero
+ expn2 = 0.0;
+ erfc2 = 0.0;
+ forcecoul2 = 0.0;
+ }
+ else {
+ rrij = lj2[itype][jtype]*r;
+ expn2 = exp(-rrij*rrij);
+ erfc2 = erfc(rrij);
+ prefactor2 = -qqrd2e*qtmp*q[j]/r;
+ forcecoul2 = prefactor2*(erfc2+EWALD_F*rrij*expn2);
+ }
+ } else forcelj = 0.0;
+
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ ecoul = prefactor*erfc1;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ ecoul = qtmp*q[j] * table;
+ }
+ if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
+ } else ecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ ecoul += prefactor2*erfc2*factor_coul;
+ evdwl = expb-lj4[itype][jtype]*r6inv-offset[itype][jtype];
+ } else evdwl = 0.0;
+
+ // Truncation, see Yaff Switch3
+ if (truncw>0) {
+ if (rsq < cut_ljsq[itype][jtype]) {
+ if (r>cut_lj[itype][jtype]-truncw) {
+ trx = (cut_lj[itype][jtype]-r)*truncwi;
+ tr = trx*trx*(3.0-2.0*trx);
+ ftr = 6.0*trx*(1.0-trx)*r*truncwi;
+ forcelj = forcelj*tr + evdwl*ftr;
+ evdwl *= tr;
+ }
+ }
+ }
+
+ fpair = (forcecoul + factor_coul*forcecoul2 + factor_lj*forcelj) * r2inv;
+ evdwl *= factor_lj;
+
+ f[i][0] += delx*fpair;
+ f[i][1] += dely*fpair;
+ f[i][2] += delz*fpair;
+ if (newton_pair || j < nlocal) {
+ f[j][0] -= delx*fpair;
+ f[j][1] -= dely*fpair;
+ f[j][2] -= delz*fpair;
+ }
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ evdwl,ecoul,fpair,delx,dely,delz);
+ }
+ }
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+
+/* ----------------------------------------------------------------------
+ allocate all arrays
+------------------------------------------------------------------------- */
+
+void PairMM3Switch3CoulGaussLong::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+
+ memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
+ memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
+ memory->create(epsilon,n+1,n+1,"pair:epsilon");
+ memory->create(sigma,n+1,n+1,"pair:sigma");
+ memory->create(gamma,n+1,n+1,"pair:gamma");
+ memory->create(lj1,n+1,n+1,"pair:lj1");
+ memory->create(lj2,n+1,n+1,"pair:lj2");
+ memory->create(lj3,n+1,n+1,"pair:lj3");
+ memory->create(lj4,n+1,n+1,"pair:lj4");
+ memory->create(offset,n+1,n+1,"pair:offset");
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+void PairMM3Switch3CoulGaussLong::settings(int narg, char **arg)
+{
+ if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
+
+ cut_lj_global = force->numeric(FLERR,arg[0]);
+ if (narg == 2) {
+ cut_coul = cut_lj_global;
+ truncw = force->numeric(FLERR,arg[1]);
+ }
+ else {
+ cut_coul = force->numeric(FLERR,arg[1]);
+ truncw = force->numeric(FLERR,arg[2]);
+ }
+ if (truncw>0.0) truncwi = 1.0/truncw;
+ else truncwi = 0.0;
+ // reset cutoffs that have been explicitly set
+
+ if (allocated) {
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++)
+ if (setflag[i][j]) cut_lj[i][j] = cut_lj_global;
+ }
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairMM3Switch3CoulGaussLong::coeff(int narg, char **arg)
+{
+ if (narg < 5 || narg > 6)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+ if (!allocated) allocate();
+
+ int ilo,ihi,jlo,jhi;
+ force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
+ force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
+
+ double epsilon_one = force->numeric(FLERR,arg[2]);
+ double sigma_one = force->numeric(FLERR,arg[3]);
+ double gamma_one = force->numeric(FLERR,arg[4]);
+
+ double cut_lj_one = cut_lj_global;
+ if (narg == 6) cut_lj_one = force->numeric(FLERR,arg[5]);
+
+ int count = 0;
+ for (int i = ilo; i <= ihi; i++) {
+ for (int j = MAX(jlo,i); j <= jhi; j++) {
+ epsilon[i][j] = epsilon_one;
+ sigma[i][j] = sigma_one;
+ gamma[i][j] = gamma_one;
+ cut_lj[i][j] = cut_lj_one;
+ setflag[i][j] = 1;
+ count++;
+ }
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairMM3Switch3CoulGaussLong::init_style()
+{
+ if (!atom->q_flag)
+ error->all(FLERR,"Pair style mm3/switch3/coulgauss/long requires atom attribute q");
+
+ // request regular or rRESPA neighbor list
+
+ int irequest;
+ int respa = 0;
+
+ if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
+ if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
+ if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
+ }
+
+ irequest = neighbor->request(this,instance_me);
+
+ if (respa >= 1) {
+ neighbor->requests[irequest]->respaouter = 1;
+ neighbor->requests[irequest]->respainner = 1;
+ }
+ if (respa == 2) neighbor->requests[irequest]->respamiddle = 1;
+
+ cut_coulsq = cut_coul * cut_coul;
+
+ // set rRESPA cutoffs
+
+ if (strstr(update->integrate_style,"respa") &&
+ ((Respa *) update->integrate)->level_inner >= 0)
+ cut_respa = ((Respa *) update->integrate)->cutoff;
+ else cut_respa = NULL;
+
+ // insure use of KSpace long-range solver, set g_ewald
+
+ if (force->kspace == NULL)
+ error->all(FLERR,"Pair style requires a KSpace style");
+ g_ewald = force->kspace->g_ewald;
+
+ // setup force tables
+
+ if (ncoultablebits) init_tables(cut_coul,cut_respa);
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairMM3Switch3CoulGaussLong::init_one(int i, int j)
+{
+ if (setflag[i][j] == 0) {
+ epsilon[i][j] = sqrt(epsilon[i][i]*epsilon[j][j]);
+ sigma[i][j] = sigma[i][i] + sigma[j][j];
+ gamma[i][j] = 1.0/sqrt(gamma[i][i]*gamma[i][i]+gamma[j][j]*gamma[j][j]);
+ cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
+ }
+
+ double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist);
+ cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
+ lj1[i][j] = 12.0 / (sigma[i][j]);
+ if (gamma[i][i]==0.0 && gamma[j][j]==0.0) lj2[i][j] = 0.0;
+ else lj2[i][j] = 1.0/sqrt(gamma[i][i]*gamma[i][i]+gamma[j][j]*gamma[j][j]);
+ lj3[i][j] = 1.84e5 * epsilon[i][j];
+ lj4[i][j] = 2.25 * epsilon[i][j] * pow(sigma[i][j],6.0);
+
+ if (offset_flag && (cut_lj[i][j] > 0.0)) {
+ // Truncation is active, so offset is zero, except if truncw==0.0
+ if (truncw==0.0) {
+ double r = cut_lj[i][j];
+ double r2inv = 1.0/(r*r);
+ double r6inv = r2inv*r2inv*r2inv;
+ double expb = lj3[i][j]*exp(-lj1[i][j]*r);
+ offset[i][j] = expb-lj4[i][j]*r6inv;
+ }
+ else {offset[i][j] = 0.0;}
+ } else offset[i][j] = 0.0;
+
+ cut_ljsq[j][i] = cut_ljsq[i][j];
+ cut_lj[j][i] = cut_lj[i][j];
+ lj1[j][i] = lj1[i][j];
+ lj2[j][i] = lj2[i][j];
+ lj3[j][i] = lj3[i][j];
+ lj4[j][i] = lj4[i][j];
+ offset[j][i] = offset[i][j];
+
+ // check interior rRESPA cutoff
+
+ if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3])
+ error->all(FLERR,"Pair cutoff < Respa interior cutoff");
+
+ // compute I,J contribution to long-range tail correction
+ // count total # of atoms of type I and J via Allreduce
+
+ if (tail_flag) {
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+
+ double count[2],all[2];
+ count[0] = count[1] = 0.0;
+ for (int k = 0; k < nlocal; k++) {
+ if (type[k] == i) count[0] += 1.0;
+ if (type[k] == j) count[1] += 1.0;
+ }
+ MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
+
+ double cg = epsilon[i][j];
+ double cg1 = cut_lj[i][j];
+ double cg3 = 2.0*sigma[i][j];//Mind the factor 2 here!!!
+ if (truncw > 0.0) {
+ double cg5 = truncw;
+ double t1 = pow(cg3, 0.2e1);
+ double t2 = t1 * cg3;
+ double t3 = 0.5e1 / 0.216e3 * t2;
+ double t5 = cg1 / 0.9e1;
+ double t8 = -cg1 + cg5;
+ double t14 = t8 * t8;
+ double t17 = 0.1e1 / cg3;
+ double t20 = exp(0.12e2 * t17 * cg5);
+ double t30 = pow(cg1, 0.2e1);
+ double t36 = exp(-0.12e2 * t17 * cg1);
+ double t37 = pow(cg5, 0.2e1);
+ double t39 = 0.1e1 / t37 / cg5;
+ double t43 = cg1 * t8;
+ double t44 = log(-t8);
+ double t47 = log(cg1);
+ double t54 = t1 * t1;
+ double t64 = cg * (0.6388888889e3 * ((-t3 + (0.7e1 / 0.36e2 * cg5 - t5) * t1 - 0.2e1 / 0.3e1 * t8 * (cg5 - cg1 / 0.4e1) * cg3 + cg5 * t14) * t20 + t3 + (cg5 / 0.12e2 + t5) * t1 + (cg5 + cg1 / 0.3e1) * cg1 * cg3 / 0.2e1 + t30 * cg5) * t2 * t36 * t39 - 0.225e1 * (0.2e1 * t43 * t44 - 0.2e1 * t43 * t47 + cg5 * (cg5 - 0.2e1 * cg1)) * t54 * t1 / cg1 / t8 * t39);
+ etail_ij = 2.0*MY_PI*all[0]*all[1]*t64;
+ ptail_ij = 2.0*MY_PI*all[0]*all[1]*t64;
+ }
+ else {
+ double t2 = pow(cg3, 0.2e1);
+ double t3 = t2 * t2;
+ double t7 = 0.12e2 / cg3 * cg1;
+ double t8 = exp(t7);
+ double t11 = pow(cg1, 0.2e1);
+ double t12 = t11 * t11;
+ double t17 = t11 * cg1;
+ double t21 = exp(-t7);
+ double t27 = -0.9259259259e-2 * cg3 * cg * (0.81e2 * t3 * cg3 * t8 - 0.1656000e7 * t12 * cg1 - 0.276000e6 * cg3 * t12 - 0.23000e5 * t2 * t17) * t21 / t17;
+ double t1 = pow(cg3, 0.2e1);
+ t2 = t1 * t1;
+ double t6 = 0.12e2 / cg3 * cg1;
+ t7 = exp(t6);
+ double t10 = pow(cg1, 0.2e1);
+ t11 = t10 * t10;
+ double t19 = t10 * cg1;
+ double t25 = exp(-t6);
+ double t29 = 0.5555555556e-1 * cg * (0.81e2 * t2 * t1 * t7 - 0.3312000e7 * t11 * t10 - 0.828000e6 * cg3 * t11 * cg1 - 0.138000e6 * t1 * t11 - 0.11500e5 * t19 * t1 * cg3) * t25 / t19;
+ etail_ij = 2.0*MY_PI*all[0]*all[1]*t27;
+ ptail_ij = -2.0/3.0*MY_PI*all[0]*all[1]*t29;
+ }
+ }
+
+ return cut;
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairMM3Switch3CoulGaussLong::write_restart(FILE *fp)
+{
+ write_restart_settings(fp);
+
+ int i,j;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ fwrite(&setflag[i][j],sizeof(int),1,fp);
+ if (setflag[i][j]) {
+ fwrite(&epsilon[i][j],sizeof(double),1,fp);
+ fwrite(&sigma[i][j],sizeof(double),1,fp);
+ fwrite(&gamma[i][j],sizeof(double),1,fp);
+ fwrite(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairMM3Switch3CoulGaussLong::read_restart(FILE *fp)
+{
+ read_restart_settings(fp);
+
+ allocate();
+
+ int i,j;
+ int me = comm->me;
+ for (i = 1; i <= atom->ntypes; i++)
+ for (j = i; j <= atom->ntypes; j++) {
+ if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+ MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
+ if (setflag[i][j]) {
+ if (me == 0) {
+ fread(&epsilon[i][j],sizeof(double),1,fp);
+ fread(&sigma[i][j],sizeof(double),1,fp);
+ fread(&gamma[i][j],sizeof(double),1,fp);
+ fread(&cut_lj[i][j],sizeof(double),1,fp);
+ }
+ MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&gamma[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to restart file
+------------------------------------------------------------------------- */
+
+void PairMM3Switch3CoulGaussLong::write_restart_settings(FILE *fp)
+{
+ fwrite(&cut_lj_global,sizeof(double),1,fp);
+ fwrite(&cut_coul,sizeof(double),1,fp);
+ fwrite(&truncw,sizeof(double),1,fp);
+ fwrite(&offset_flag,sizeof(int),1,fp);
+ fwrite(&mix_flag,sizeof(int),1,fp);
+ fwrite(&tail_flag,sizeof(int),1,fp);
+ fwrite(&ncoultablebits,sizeof(int),1,fp);
+ fwrite(&tabinner,sizeof(double),1,fp);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 reads from restart file, bcasts
+------------------------------------------------------------------------- */
+
+void PairMM3Switch3CoulGaussLong::read_restart_settings(FILE *fp)
+{
+ if (comm->me == 0) {
+ fread(&cut_lj_global,sizeof(double),1,fp);
+ fread(&cut_coul,sizeof(double),1,fp);
+ fread(&truncw,sizeof(double),1,fp);
+ fread(&offset_flag,sizeof(int),1,fp);
+ fread(&mix_flag,sizeof(int),1,fp);
+ fread(&tail_flag,sizeof(int),1,fp);
+ fread(&ncoultablebits,sizeof(int),1,fp);
+ fread(&tabinner,sizeof(double),1,fp);
+ }
+ printf("Reading from restart, trunc = %f\n",truncw);
+ MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&truncw,1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
+ MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
+ MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
+}
+
+
+/* ----------------------------------------------------------------------
+ proc 0 writes to data file
+------------------------------------------------------------------------- */
+
+void PairMM3Switch3CoulGaussLong::write_data(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ fprintf(fp,"%d %g %g %g\n",i,epsilon[i][i],sigma[i][i],gamma[i][i]);
+}
+
+/* ----------------------------------------------------------------------
+ proc 0 writes all pairs to data file
+------------------------------------------------------------------------- */
+
+void PairMM3Switch3CoulGaussLong::write_data_all(FILE *fp)
+{
+ for (int i = 1; i <= atom->ntypes; i++)
+ for (int j = i; j <= atom->ntypes; j++)
+ fprintf(fp,"%d %d %g %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],gamma[i][j],cut_lj[i][j]);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairMM3Switch3CoulGaussLong::single(int i, int j, int itype, int jtype,
+ double rsq,
+ double factor_coul, double factor_lj,
+ double &fforce)
+{
+ double r2inv,r6inv,r,grij,expm2,t,erfc1,prefactor,prefactor2,rrij,expn2,erfc2;
+ double fraction,table,forcecoul,forcecoul2,forcelj,phicoul,phicoul2,philj;
+ double expb, ecoul, evdwl, trx, tr, ftr;
+
+ int itable;
+
+ r2inv = 1.0/rsq;
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq) {
+ r = sqrt(rsq);
+ grij = g_ewald * r;
+ expm2 = exp(-grij*grij);
+ t = 1.0 / (1.0 + EWALD_P*grij);
+ erfc1 = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
+ prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
+ forcecoul = prefactor * (erfc1 + EWALD_F*grij*expm2);
+ if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
+ } else {
+ union_int_float_t rsq_lookup_single;
+ rsq_lookup_single.f = rsq;
+ itable = rsq_lookup_single.i & ncoulmask;
+ itable >>= ncoulshiftbits;
+ fraction = (rsq_lookup_single.f - rtable[itable]) * drtable[itable];
+ table = ftable[itable] + fraction*dftable[itable];
+ forcecoul = atom->q[i]*atom->q[j] * table;
+ if (factor_coul < 1.0) {
+ table = ctable[itable] + fraction*dctable[itable];
+ prefactor = atom->q[i]*atom->q[j] * table;
+ forcecoul -= (1.0-factor_coul)*prefactor;
+ }
+ }
+ } else forcecoul = 0.0;
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ r = sqrt(rsq);
+ r6inv = r2inv*r2inv*r2inv;
+ expb = lj3[itype][jtype]*exp(-lj1[itype][jtype]*r);
+ rrij = lj2[itype][jtype] * r;
+ if (rrij==0.0) {
+ expn2 = 0.0;
+ erfc2 = 0.0;
+ }
+ else {
+ expn2 = exp(-rrij*rrij);
+ erfc2 = erfc(rrij);
+ }
+ prefactor2 = -force->qqrd2e * atom->q[i]*atom->q[j]/r;
+ forcecoul2 = prefactor2 * (erfc2 + EWALD_F*rrij*expn2);
+ forcelj = expb*lj1[itype][jtype]*r-6.0*lj4[itype][jtype]*r6inv;
+ } else forcelj = 0.0;
+
+ double eng = 0.0;
+ if (rsq < cut_coulsq) {
+ if (!ncoultablebits || rsq <= tabinnersq)
+ phicoul = prefactor*erfc1;
+ else {
+ table = etable[itable] + fraction*detable[itable];
+ phicoul = atom->q[i]*atom->q[j] * table;
+ }
+ if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
+ eng += phicoul;
+ }
+
+ if (rsq < cut_ljsq[itype][jtype]) {
+ ecoul += prefactor2*erfc2*factor_coul;
+ evdwl = expb-lj4[itype][jtype]*r6inv-offset[itype][jtype];
+ } else evdwl = 0.0;
+
+ // Truncation, see Yaff Switch3
+ if (truncw>0) {
+ if (rsq < cut_ljsq[itype][jtype]) {
+ if (r>cut_lj[itype][jtype]-truncw) {
+ trx = (cut_lj[itype][jtype]-r)*truncwi;
+ tr = trx*trx*(3.0-2.0*trx);
+ ftr = 6.0*trx*(1.0-trx)*r*truncwi;
+ forcelj = forcelj*tr + evdwl*ftr;
+ evdwl *= tr;
+ }
+ }
+ }
+ eng += evdwl*factor_lj;
+ fforce = (forcecoul + factor_coul*forcecoul2 + factor_lj*forcelj) * r2inv;
+
+ return eng;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void *PairMM3Switch3CoulGaussLong::extract(const char *str, int &dim)
+{
+ dim = 0;
+ if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
+ dim = 2;
+ if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
+ if (strcmp(str,"sigma") == 0) return (void *) sigma;
+ if (strcmp(str,"gamma") == 0) return (void *) gamma;
+ return NULL;
+}
diff --git a/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h
new file mode 100644
index 0000000000000000000000000000000000000000..35ae6c7995c927a4dd540efb063f5af0ebb3e053
--- /dev/null
+++ b/src/USER-YAFF/pair_mm3_switch3_coulgauss_long.h
@@ -0,0 +1,91 @@
+/* -*- c++ -*- ----------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(mm3/switch3/coulgauss/long,PairMM3Switch3CoulGaussLong)
+
+#else
+
+#ifndef LMP_PAIR_MM3_SWITCH3_COULGAUSS_LONG_H
+#define LMP_PAIR_MM3_SWITCH3_COULGAUSS_LONG_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairMM3Switch3CoulGaussLong : public Pair {
+
+ public:
+ PairMM3Switch3CoulGaussLong(class LAMMPS *);
+ virtual ~PairMM3Switch3CoulGaussLong();
+ virtual void compute(int, int);
+ virtual void settings(int, char **);
+ void coeff(int, char **);
+ virtual void init_style();
+ virtual double init_one(int, int);
+ void write_restart(FILE *);
+ void read_restart(FILE *);
+ virtual void write_restart_settings(FILE *);
+ virtual void read_restart_settings(FILE *);
+ void write_data(FILE *);
+ void write_data_all(FILE *);
+ virtual double single(int, int, int, int, double, double, double, double &);
+
+ virtual void *extract(const char *, int &);
+
+ protected:
+ double cut_lj_global;
+ double truncw, truncwi;
+ double **cut_lj,**cut_ljsq;
+ double cut_coul,cut_coulsq;
+ double **epsilon,**sigma,**gamma;
+ double **lj1,**lj2,**lj3,**lj4,**offset;
+ double *cut_respa;
+ double qdist; // TIP4P distance from O site to negative charge
+ double g_ewald;
+
+ virtual void allocate();
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Incorrect args for pair coefficients
+
+Self-explanatory. Check the input script or data file.
+
+E: Pair style mm3/switch3/coulgauss/long requires atom attribute q
+
+The atom style defined does not have this attribute.
+
+E: Pair style requires a KSpace style
+
+No kspace style is defined.
+
+E: Pair cutoff < Respa interior cutoff
+
+One or more pairwise cutoffs are too short to use with the specified
+rRESPA cutoffs.
+
+*/