diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index b3bae8fd4a8d5e8be4d0af9dd45821a093812888..6471fb73780bb8b05da980b23d4de943d60035ea 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/PDF/USER-CGDNA.pdf b/doc/src/PDF/USER-CGDNA.pdf
index 843bba00d5c5a707577d07dda1929ba4c8a07987..7fcf3660156a903ec1ea7ec984ef4f8b11c73bbe 100644
Binary files a/doc/src/PDF/USER-CGDNA.pdf and b/doc/src/PDF/USER-CGDNA.pdf differ
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/fix_bond_react.txt b/doc/src/fix_bond_react.txt
index 8f71cd14ec7c4a405cd6f752db30ba7b37100e14..c5b07bb973310f3451bc9ae52a6853e4b8151e6e 100644
--- a/doc/src/fix_bond_react.txt
+++ b/doc/src/fix_bond_react.txt
@@ -36,10 +36,12 @@ react = mandatory argument indicating new reaction specification :l
template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l
zero or more individual keyword/value pairs may be appended to each react argument :l
- individual_keyword = {prob} or {stabilize_steps} or {update_edges} :l
+ individual_keyword = {prob} or {max_rxn} or {stabilize_steps} or {update_edges} :l
{prob} values = fraction seed
fraction = initiate reaction with this probability if otherwise eligible
seed = random number seed (positive integer)
+ {max_rxn} value = N
+ N = maximum number of reactions allowed to occur
{stabilize_steps} value = timesteps
timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms
{update_edges} value = {none} or {charges} or {custom}
@@ -142,7 +144,7 @@ modified to match the post-reaction template.
A bonding atom pair will be identified if several conditions are met.
First, a pair of atoms I,J within the specified react-group-ID of type
-itype and jtype must separated by a distance between {Rmin} and
+itype and jtype must be separated by a distance between {Rmin} and
{Rmax}. It is possible that multiple bonding atom pairs are
identified: if the bonding atoms in the pre-reacted template are not
1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
@@ -211,9 +213,10 @@ mandatory keyword is 'equivalences' and the optional keywords are
N {equivalences} = # of atoms N in the reaction molecule templates
N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
N {deleteIDs} = # of atoms N that are specified for deletion
-N {customIDs} = # of atoms N that are specified for a custom update :pre
+N {customIDs} = # of atoms N that are specified for a custom update
+N {constraints} = # of specified reaction constraints N :pre
-The body of the map file contains two mandatory sections and three
+The body of the map file contains two mandatory sections and four
optional sections. The first mandatory section begins with the keyword
'BondingIDs' and lists the atom IDs of the bonding atom pair in the
pre-reacted molecule template. The second mandatory section begins
@@ -230,7 +233,10 @@ Edges' and allows for forcing the update of a specific atom's atomic
charge. The first column is the ID of an atom near the edge of the
pre-reacted molecule template, and the value of the second column is
either 'none' or 'charges.' Further details are provided in the
-discussion of the 'update_edges' keyword.
+discussion of the 'update_edges' keyword. The fourth optional section
+begins with the keyword 'Constraints' and lists additional criteria
+that must be satisfied in order for the reaction to occur. Currently,
+there is one type of constraint available, as discussed below.
A sample map file is given below:
@@ -263,6 +269,18 @@ Equivalences :pre
:line
+Any number of additional constraints may be specified in the
+Constraints section of the map file. Currently there is one type of
+additional constraint, of type 'distance', whose syntax is as follows:
+
+distance {ID1} {ID2} {rmin} {rmax} :pre
+
+where 'distance' is the required keyword, {ID1} and {ID2} are
+pre-reaction atom IDs, and these two atoms must be separated by a
+distance between {rmin} and {rmax} for the reaction to occur. This
+constraint can be used to enforce a certain orientation between
+reacting molecules.
+
Once a reaction site has been successfully identified, data structures
within LAMMPS that store bond topology are updated to reflect the
post-reacted molecule template. All force fields with fixed bonds,
@@ -285,7 +303,8 @@ The {prob} keyword can affect whether an eligible reaction actually
occurs. The fraction setting must be a value between 0.0 and 1.0. A
uniform random number between 0.0 and 1.0 is generated and the
eligible reaction only occurs if the random number is less than the
-fraction.
+fraction. Up to N reactions are permitted to occur, as optionally
+specified by the {max_rxn} keyword.
The {stabilize_steps} keyword allows for the specification of how many
timesteps a reaction site is stabilized before being returned to the
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/misc/entropy/log.entropy b/examples/USER/misc/entropy/log.entropy
index c380c62a731b77c6c83d3a36fc822b52843f8c17..333214ada8839480c975a1fc57ca6b9a5758640f 100644
--- a/examples/USER/misc/entropy/log.entropy
+++ b/examples/USER/misc/entropy/log.entropy
@@ -1,4 +1,4 @@
-LAMMPS (30 Mar 2018)
+LAMMPS (4 Jan 2019)
units metal
atom_style full
@@ -45,10 +45,10 @@ fix 1 all nph x 1. 1. 10.
fix 2 all temp/csvr 350. 350. 0.1 64582
run 1000
-WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
-WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
-WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
-WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:138)
+WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
+WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
+WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
+WARNING: More than one compute entropy/atom (../compute_entropy_atom.cpp:139)
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
@@ -56,27 +56,27 @@ Neighbor list info ...
ghost atom cutoff = 13.2
binsize = 6.6, bins = 21 6 6
5 neighbor lists, perpetual/occasional/extra = 5 0 0
- (1) pair eam/fs, perpetual
+ (1) pair eam/fs, perpetual, half/full from (2)
attributes: half, newton on
- pair build: half/bin/newton/tri
- stencil: half/bin/3d/newton/tri
- bin: standard
+ pair build: halffull/newton
+ stencil: none
+ bin: none
(2) compute entropy/atom, perpetual
- attributes: full, newton on, ghost
- pair build: full/bin/ghost
- stencil: full/ghost/bin/3d
+ attributes: full, newton on
+ pair build: full/bin
+ stencil: full/bin/3d
bin: standard
(3) compute entropy/atom, perpetual, copy from (2)
- attributes: full, newton on, ghost
+ attributes: full, newton on
pair build: copy
stencil: none
bin: none
- (4) compute entropy/atom, perpetual, copy from (2)
+ (4) compute entropy/atom, perpetual
attributes: full, newton on, ghost
- pair build: copy
- stencil: none
- bin: none
- (5) compute entropy/atom, perpetual, copy from (2)
+ pair build: full/bin/ghost
+ stencil: full/ghost/bin/3d
+ bin: standard
+ (5) compute entropy/atom, perpetual, copy from (4)
attributes: full, newton on, ghost
pair build: copy
stencil: none
@@ -85,34 +85,34 @@ Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.002
-Per MPI rank memory allocation (min/avg/max) = 25.68 | 25.69 | 25.69 Mbytes
+Per MPI rank memory allocation (min/avg/max) = 19.6 | 19.6 | 19.6 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 346.29871 -4285.222 0 -4101.9191 594.65353 165399.75
- 500 359.33758 -4285.247 0 -4095.0423 471.98587 165847.18
- 1000 348.99659 -4276.2274 0 -4091.4964 149.27188 166966.18
-Loop time of 5.3437 on 4 procs for 1000 steps with 4096 atoms
+ 500 359.33769 -4285.2472 0 -4095.0424 472.02043 165847.09
+ 1000 348.99683 -4276.2282 0 -4091.4971 149.38771 166965.86
+Loop time of 4.4394 on 4 procs for 1000 steps with 4096 atoms
-Performance: 32.337 ns/day, 0.742 hours/ns, 187.136 timesteps/s
-99.8% CPU use with 4 MPI tasks x no OpenMP threads
+Performance: 38.924 ns/day, 0.617 hours/ns, 225.256 timesteps/s
+99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
-Pair | 4.2832 | 4.3257 | 4.3839 | 1.8 | 80.95
-Bond | 0.00018309 | 0.00019825 | 0.00021418 | 0.0 | 0.00
-Neigh | 0.42195 | 0.42512 | 0.42739 | 0.3 | 7.96
-Comm | 0.051679 | 0.1101 | 0.14916 | 10.8 | 2.06
-Output | 0.40909 | 0.4091 | 0.40911 | 0.0 | 7.66
-Modify | 0.060869 | 0.061921 | 0.06327 | 0.4 | 1.16
-Other | | 0.01161 | | | 0.22
+Pair | 3.5298 | 3.5931 | 3.6669 | 2.6 | 80.94
+Bond | 8.2099e-05 | 0.00011444 | 0.00014673 | 0.0 | 0.00
+Neigh | 0.43384 | 0.4445 | 0.45558 | 1.4 | 10.01
+Comm | 0.048904 | 0.11122 | 0.16728 | 12.7 | 2.51
+Output | 0.22595 | 0.22595 | 0.22596 | 0.0 | 5.09
+Modify | 0.053103 | 0.053795 | 0.054549 | 0.3 | 1.21
+Other | | 0.01068 | | | 0.24
Nlocal: 1024 ave 1040 max 1001 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 4614.25 ave 4700 max 4540 min
Histogram: 1 1 0 0 0 0 0 1 0 1
-Neighs: 121747 ave 126398 max 116931 min
+Neighs: 121747 ave 126398 max 116930 min
Histogram: 1 0 0 1 0 0 1 0 0 1
-FullNghs: 243494 ave 252523 max 233842 min
+FullNghs: 243494 ave 252523 max 233841 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 973974
@@ -121,4 +121,4 @@ Ave special neighs/atom = 0
Neighbor list builds = 13
Dangerous builds = 0
-Total wall time: 0:00:05
+Total wall time: 0:00:04
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
+ 22 cross 183.45287073 91.94550669 91.94550669 1.27905582 1.27905582 124.82435184
+ 23 harmonic 16.58040240 109.62517017
+ 24 harmonic 17.35339453 114.44875517
+ 25 harmonic 17.77569321 132.30806010
+ 26 harmonic 31.05808424 89.91290461
+ 27 harmonic 35.90327756 119.61990442
+ 28 harmonic 65.78425626 120.00645318
+ 29 harmonic 31.59874504 120.45871258
+ 30 harmonic 43.33676649 120.04493381
+ 31 harmonic 62.87326877 119.94842490
+ 32 harmonic 75.47920221 117.59298491
+ 33 harmonic 76.76979213 124.86144100
+ 34 cosine/squared 1689.15160421 180.00000000
+
+Dihedral Coeffs
+
+ 1 1 3.73165017 2 -180.00000000
+ 2 1 2.24530337 2 -180.00000000
+ 3 1 4.66917332 2 -180.00000000
+ 4 1 3.98899930 2 -180.00000000
+ 5 1 3.29635668 2 -180.00000000
+ 6 1 1.54619053 2 -180.00000000
+ 7 1 3.86252462 2 -180.00000000
+ 8 1 2.05124797 2 -180.00000000
+ 9 1 2.35456853 2 -180.00000000
+
+Improper Coeffs
+
+ 1 9.10278571 0.00000000
+ 2 167.11786187 0.00000000
+ 3 18.17859622 0.00000000
+
+Pair Coeffs
+
+ 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
+
+Atoms
+
+ 1 1 1 -1.2098756939999999460155777342151850 6.7153870720493431534237060986924917 4.2828041318282634719594170746859163 8.5866133816897338704166031675413251
+ 2 1 1 -1.2098756939999999460155777342151850 13.3783843949194771738575582276098430 4.2828041318282634719594170746859163 8.5866133816897338704166031675413251
+ 3 1 1 -1.2098756939999999460155777342151850 3.5035237129981489090368995675817132 12.8223120918310673488349493709392846 2.3141018836642901490563417610246688
+ 4 1 1 -1.2098756939999999460155777342151850 10.1665216355380785273609944852069020 12.8223120918310673488349493709392846 2.3141018836642901490563417610246688
+ 5 1 1 -1.2098756939999999460155777342151850 6.8349996196255871083735655702184886 12.8213427865959719298416530364193022 3.9586200971404887916094139654887840
+ 6 1 1 -1.2098756939999999460155777342151850 13.4979977420554568823263252852484584 12.8213427865959701534848136361688375 3.9586200971404887916094139654887840
+ 7 1 1 -1.2098756939999999460155777342151850 3.3839079367670850118088310409802943 4.2840038831740319125174210057593882 10.2311117738051464698401105124503374
+ 8 1 1 -1.2098756939999999460155777342151850 10.0469052596372208085995225701481104 4.2840038831740310243390013056341559 10.2311117738051464698401105124503374
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+
+Impropers
+
+ 1 3 89 49 122 93
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+ 62 2 150 34 21 134
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+ 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
+
+Atoms
+
+ 1 1 1 1.1385908011000001049950469678151421 7.7681655356393379818769062694627792 5.4353470464458997213341717724688351 5.4353481400207055429518732125870883
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+ 1234 11 10 34 32 115
+ 1235 11 10 34 32 128
+ 1236 11 10 34 32 96
+ 1237 9 32 96 168 111
+ 1238 10 32 96 168 312
+ 1239 9 18 111 168 96
+ 1240 10 18 111 168 312
+ 1241 9 115 174 102 10
+ 1242 10 318 174 102 10
+ 1243 10 32 115 174 318
+ 1244 9 32 115 174 102
+ 1245 9 32 128 184 131
+ 1246 10 32 128 184 328
+ 1247 9 2 131 184 128
+ 1248 10 2 131 184 328
+
+Impropers
+
+ 1 2 137 41 281 68
+ 2 2 138 42 67 282
+ 3 2 139 66 43 283
+ 4 2 140 65 284 44
+ 5 2 141 285 45 70
+ 6 2 142 69 46 286
+ 7 2 143 287 47 72
+ 8 2 144 288 71 48
+ 9 2 145 49 289 88
+ 10 2 146 50 87 290
+ 11 2 147 51 291 86
+ 12 2 148 292 52 85
+ 13 2 149 82 53 293
+ 14 2 150 81 54 294
+ 15 2 151 84 295 55
+ 16 2 152 83 296 56
+ 17 2 153 57 297 78
+ 18 2 154 58 77 298
+ 19 2 155 59 299 80
+ 20 2 156 300 60 79
+ 21 2 157 301 76 61
+ 22 2 158 75 62 302
+ 23 2 159 74 303 63
+ 24 2 160 73 304 64
+ 25 2 161 89 305 108
+ 26 2 162 306 107 90
+ 27 2 163 106 91 307
+ 28 2 164 105 92 308
+ 29 2 165 93 309 110
+ 30 2 166 109 310 94
+ 31 2 167 95 311 112
+ 32 2 168 96 111 312
+ 33 2 169 97 313 118
+ 34 2 170 314 117 98
+ 35 2 171 315 99 120
+ 36 2 172 316 100 119
+ 37 2 173 101 116 317
+ 38 2 174 115 318 102
+ 39 2 175 114 319 103
+ 40 2 176 113 104 320
+ 41 2 177 121 321 136
+ 42 2 178 322 135 122
+ 43 2 179 323 123 134
+ 44 2 180 124 324 133
+ 45 2 181 125 325 130
+ 46 2 182 129 326 126
+ 47 2 183 132 127 327
+ 48 2 184 131 128 328
+ 49 3 185 329 281 188
+ 50 3 186 282 187 330
+ 51 3 187 186 331 283
+ 52 3 188 185 284 332
+ 53 3 189 333 285 192
+ 54 3 190 286 191 334
+ 55 3 191 335 190 287
+ 56 3 192 288 189 336
+ 57 3 193 289 337 196
+ 58 3 194 290 195 338
+ 59 3 195 194 339 291
+ 60 3 196 193 340 292
+ 61 3 197 293 341 200
+ 62 3 198 342 199 294
+ 63 3 199 343 198 295
+ 64 3 200 344 197 296
+ 65 3 201 297 345 204
+ 66 3 202 346 203 298
+ 67 3 203 202 347 299
+ 68 3 204 201 300 348
+ 69 3 205 349 301 208
+ 70 3 206 350 207 302
+ 71 3 207 351 206 303
+ 72 3 208 304 205 352
+ 73 3 209 353 284 212
+ 74 3 210 354 211 283
+ 75 3 211 210 355 282
+ 76 3 212 209 281 356
+ 77 3 213 357 286 216
+ 78 3 214 285 358 215
+ 79 3 215 214 359 288
+ 80 3 216 213 287 360
+ 81 3 217 361 220 304
+ 82 3 218 362 219 303
+ 83 3 219 218 363 302
+ 84 3 220 217 364 301
+ 85 3 221 298 365 224
+ 86 3 222 297 366 223
+ 87 3 223 300 222 367
+ 88 3 224 299 221 368
+ 89 3 225 369 228 294
+ 90 3 226 370 227 293
+ 91 3 227 226 371 296
+ 92 3 228 225 372 295
+ 93 3 229 292 373 232
+ 94 3 230 291 374 231
+ 95 3 231 290 230 375
+ 96 3 232 289 229 376
+ 97 3 233 305 377 236
+ 98 3 234 306 235 378
+ 99 3 235 234 307 379
+ 100 3 236 233 380 308
+ 101 3 237 381 309 240
+ 102 3 238 310 239 382
+ 103 3 239 383 238 311
+ 104 3 240 384 237 312
+ 105 3 241 313 385 244
+ 106 3 242 314 243 386
+ 107 3 243 242 315 387
+ 108 3 244 241 316 388
+ 109 3 245 317 389 248
+ 110 3 246 318 247 390
+ 111 3 247 246 319 391
+ 112 3 248 320 245 392
+ 113 3 249 393 308 252
+ 114 3 250 394 251 307
+ 115 3 251 250 395 306
+ 116 3 252 249 305 396
+ 117 3 253 397 310 256
+ 118 3 254 309 398 255
+ 119 3 255 254 399 312
+ 120 3 256 253 311 400
+ 121 3 257 401 260 320
+ 122 3 258 402 259 319
+ 123 3 259 258 403 318
+ 124 3 260 257 404 317
+ 125 3 261 314 405 264
+ 126 3 262 313 406 263
+ 127 3 263 316 262 407
+ 128 3 264 315 261 408
+ 129 3 265 321 409 268
+ 130 3 266 322 267 410
+ 131 3 267 266 323 411
+ 132 3 268 265 324 412
+ 133 3 269 413 325 272
+ 134 3 270 326 271 414
+ 135 3 271 270 327 415
+ 136 3 272 416 269 328
+ 137 3 273 417 276 326
+ 138 3 274 418 275 325
+ 139 3 275 274 419 328
+ 140 3 276 273 420 327
+ 141 3 277 324 421 280
+ 142 3 278 323 422 279
+ 143 3 279 322 278 423
+ 144 3 280 321 277 424
+ 145 1 281 137 185 212
+ 146 1 282 138 211 186
+ 147 1 283 210 139 187
+ 148 1 284 209 140 188
+ 149 1 285 189 141 214
+ 150 1 286 213 142 190
+ 151 1 287 191 143 216
+ 152 1 288 192 215 144
+ 153 1 289 145 193 232
+ 154 1 290 146 231 194
+ 155 1 291 147 195 230
+ 156 1 292 148 229 196
+ 157 1 293 197 149 226
+ 158 1 294 225 150 198
+ 159 1 295 228 199 151
+ 160 1 296 227 200 152
+ 161 1 297 153 201 222
+ 162 1 298 154 221 202
+ 163 1 299 155 203 224
+ 164 1 300 156 223 204
+ 165 1 301 205 220 157
+ 166 1 302 219 158 206
+ 167 1 303 218 207 159
+ 168 1 304 217 208 160
+ 169 1 305 161 233 252
+ 170 1 306 162 251 234
+ 171 1 307 250 163 235
+ 172 1 308 249 164 236
+ 173 1 309 237 165 254
+ 174 1 310 253 166 238
+ 175 1 311 239 167 256
+ 176 1 312 240 255 168
+ 177 1 313 241 169 262
+ 178 1 314 170 261 242
+ 179 1 315 243 171 264
+ 180 1 316 172 263 244
+ 181 1 317 245 260 173
+ 182 1 318 259 246 174
+ 183 1 319 258 247 175
+ 184 1 320 257 176 248
+ 185 1 321 265 177 280
+ 186 1 322 178 279 266
+ 187 1 323 267 278 179
+ 188 1 324 268 180 277
+ 189 1 325 269 181 274
+ 190 1 326 273 270 182
+ 191 1 327 276 271 183
+ 192 1 328 275 184 272
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/KOKKOS/pair_snap_kokkos_impl.h b/src/KOKKOS/pair_snap_kokkos_impl.h
index c452042cfecbd5730a2a35cfda2c5fc64e5eaecf..998e75fabe80ffa69b54c655ee42917ff47b0fc4 100644
--- a/src/KOKKOS/pair_snap_kokkos_impl.h
+++ b/src/KOKKOS/pair_snap_kokkos_impl.h
@@ -256,7 +256,6 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
if (vflag_fdotr) pair_virial_fdotr_compute(this);
-
if (eflag_atom) {
k_eatom.template modify<DeviceType>();
k_eatom.template sync<LMPHostType>();
@@ -275,8 +274,8 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
// free duplicated memory
if (need_dup) {
- dup_f = decltype(dup_f)();
- dup_vatom = decltype(dup_vatom)();
+ dup_f = decltype(dup_f)();
+ dup_vatom = decltype(dup_vatom)();
}
}
@@ -453,6 +452,13 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
//t4 += timer.seconds(); timer.reset();
team.team_barrier();
+ if (quadraticflag) {
+ my_sna.compute_bi(team);
+ team.team_barrier();
+ my_sna.copy_bi2bvec(team);
+ team.team_barrier();
+ }
+
// for neighbors of I within cutoff:
// compute dUi/drj and dBi/drj
// Fij = dEi/dRj = -dEi/dRi => add to Fi, subtract from Fj
@@ -472,10 +478,6 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
my_sna.compute_dbidrj(team);
//t7 += timer2.seconds(); timer2.reset();
my_sna.copy_dbi2dbvec(team);
- if (quadraticflag) {
- my_sna.compute_bi(team);
- my_sna.copy_bi2bvec(team);
- }
Kokkos::single(Kokkos::PerThread(team), [&] (){
F_FLOAT fij[3];
@@ -536,10 +538,10 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
a_f(j,1) -= fij[1];
a_f(j,2) -= fij[2];
- // tally per-atom virial contribution
+ // tally global and per-atom virial contribution
if (EVFLAG) {
- if (vflag) {
+ if (vflag_either) {
v_tally_xyz<NEIGHFLAG>(ev,i,j,
fij[0],fij[1],fij[2],
-my_sna.rij(jj,0),-my_sna.rij(jj,1),
@@ -554,11 +556,13 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
// tally energy contribution
if (EVFLAG) {
- if (eflag) {
+ if (eflag_either) {
if (!quadraticflag) {
my_sna.compute_bi(team);
+ team.team_barrier();
my_sna.copy_bi2bvec(team);
+ team.team_barrier();
}
// E = beta.B + 0.5*B^t.alpha.B
@@ -566,14 +570,15 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
// coeff[k] = alpha_ii or
// coeff[k] = alpha_ij = alpha_ji, j != i
- if (team.team_rank() == 0)
- Kokkos::single(Kokkos::PerThread(team), [&] () {
+ Kokkos::single(Kokkos::PerTeam(team), [&] () {
+
+ // evdwl = energy of atom I, sum over coeffs_k * Bi_k
- // evdwl = energy of atom I, sum over coeffs_k * Bi_k
+ double evdwl = d_coeffi[0];
- double evdwl = d_coeffi[0];
+ // linear contributions
+ // could use thread vector range on this loop
- // linear contributions
for (int k = 1; k <= ncoeff; k++)
evdwl += d_coeffi[k]*my_sna.bvec[k-1];
@@ -589,11 +594,10 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAP<NEIGHFLAG,EVFLAG>,const
}
}
}
-// ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0);
- if (eflag_either) {
- if (eflag_global) ev.evdwl += evdwl;
- if (eflag_atom) d_eatom[i] += evdwl;
- }
+
+ //ev_tally_full(i,2.0*evdwl,0.0,0.0,0.0,0.0,0.0);
+ if (eflag_global) ev.evdwl += evdwl;
+ if (eflag_atom) d_eatom[i] += evdwl;
});
}
}
diff --git a/src/KOKKOS/sna_kokkos_impl.h b/src/KOKKOS/sna_kokkos_impl.h
index 25561fef5d0decf60f4ab6d74d3e8cf20693c9ff..6a19c578293665060cc38a8eec41a10a7747b3c0 100644
--- a/src/KOKKOS/sna_kokkos_impl.h
+++ b/src/KOKKOS/sna_kokkos_impl.h
@@ -327,29 +327,40 @@ void SNAKokkos<DeviceType>::compute_bi(const typename Kokkos::TeamPolicy<DeviceT
clock_gettime(CLOCK_REALTIME, &starttime);
#endif
- Kokkos::parallel_for(Kokkos::ThreadVectorRange(team,idxj_max),
+ Kokkos::parallel_for(Kokkos::TeamThreadRange(team,idxj_full_max),
[&] (const int& idx) {
- const int j1 = idxj(idx).j1;
- const int j2 = idxj(idx).j2;
- const int j = idxj(idx).j;
- double b_j1_j2_j = 0.0;
+ const int j1 = idxj_full(idx).j1;
+ const int j2 = idxj_full(idx).j2;
+ const int j = idxj_full(idx).j;
- for(int mb = 0; 2*mb < j; mb++)
- for(int ma = 0; ma <= j; ma++) {
- b_j1_j2_j +=
+ const int bound = (j+2)/2;
+ double b_j1_j2_j = 0.0;
+ double b_j1_j2_j_temp = 0.0;
+ Kokkos::parallel_reduce(Kokkos::ThreadVectorRange(team,(j+1)*bound),
+ [&] (const int mbma, double& sum) {
+ //for(int mb = 0; 2*mb <= j; mb++)
+ //for(int ma = 0; ma <= j; ma++) {
+ const int ma = mbma%(j+1);
+ const int mb = mbma/(j+1);
+ if (2*mb == j) return;
+ sum +=
uarraytot_r(j,ma,mb) * zarray_r(j1,j2,j,mb,ma) +
uarraytot_i(j,ma,mb) * zarray_i(j1,j2,j,mb,ma);
- } // end loop over ma, mb
+ },b_j1_j2_j_temp); // end loop over ma, mb
+ b_j1_j2_j += b_j1_j2_j_temp;
// For j even, special treatment for middle column
if (j%2 == 0) {
const int mb = j/2;
- for(int ma = 0; ma < mb; ma++) {
- b_j1_j2_j +=
+ Kokkos::parallel_reduce(Kokkos::ThreadVectorRange(team, mb),
+ [&] (const int ma, double& sum) {
+ //for(int ma = 0; ma < mb; ma++) {
+ sum +=
uarraytot_r(j,ma,mb) * zarray_r(j1,j2,j,mb,ma) +
uarraytot_i(j,ma,mb) * zarray_i(j1,j2,j,mb,ma);
- }
+ },b_j1_j2_j_temp); // end loop over ma
+ b_j1_j2_j += b_j1_j2_j_temp;
const int ma = mb;
b_j1_j2_j +=
@@ -357,11 +368,13 @@ void SNAKokkos<DeviceType>::compute_bi(const typename Kokkos::TeamPolicy<DeviceT
uarraytot_i(j,ma,mb) * zarray_i(j1,j2,j,mb,ma))*0.5;
}
- b_j1_j2_j *= 2.0;
- if (bzero_flag)
- b_j1_j2_j -= bzero[j];
+ Kokkos::single(Kokkos::PerThread(team), [&] () {
+ b_j1_j2_j *= 2.0;
+ if (bzero_flag)
+ b_j1_j2_j -= bzero[j];
- barray(j1,j2,j) = b_j1_j2_j;
+ barray(j1,j2,j) = b_j1_j2_j;
+ });
});
//} // end loop over j
//} // end loop over j1, j2
@@ -1028,6 +1041,8 @@ void SNAKokkos<DeviceType>::create_team_scratch_arrays(const typename Kokkos::Te
uarraytot_i_a = uarraytot_i = t_sna_3d(team.team_scratch(1),jdim,jdim,jdim);
zarray_r = t_sna_5d(team.team_scratch(1),jdim,jdim,jdim,jdim,jdim);
zarray_i = t_sna_5d(team.team_scratch(1),jdim,jdim,jdim,jdim,jdim);
+ bvec = Kokkos::View<double*, Kokkos::LayoutRight, DeviceType>(team.team_scratch(1),ncoeff);
+ barray = t_sna_3d(team.team_scratch(1),jdim,jdim,jdim);
rij = t_sna_2d(team.team_scratch(1),nmax,3);
rcutij = t_sna_1d(team.team_scratch(1),nmax);
@@ -1046,6 +1061,8 @@ T_INT SNAKokkos<DeviceType>::size_team_scratch_arrays() {
size += t_sna_3d::shmem_size(jdim,jdim,jdim); // uarraytot_i_a
size += t_sna_5d::shmem_size(jdim,jdim,jdim,jdim,jdim); // zarray_r
size += t_sna_5d::shmem_size(jdim,jdim,jdim,jdim,jdim); // zarray_i
+ size += Kokkos::View<double*, Kokkos::LayoutRight, DeviceType>::shmem_size(ncoeff); // bvec
+ size += t_sna_3d::shmem_size(jdim,jdim,jdim); // barray
size += t_sna_2d::shmem_size(nmax,3); // rij
size += t_sna_1d::shmem_size(nmax); // rcutij
@@ -1062,8 +1079,6 @@ KOKKOS_INLINE_FUNCTION
void SNAKokkos<DeviceType>::create_thread_scratch_arrays(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team)
{
int jdim = twojmax + 1;
- bvec = Kokkos::View<double*, Kokkos::LayoutRight, DeviceType>(team.thread_scratch(1),ncoeff);
- barray = t_sna_3d(team.thread_scratch(1),jdim,jdim,jdim);
dbvec = Kokkos::View<double*[3], Kokkos::LayoutRight, DeviceType>(team.thread_scratch(1),ncoeff);
dbarray = t_sna_4d(team.thread_scratch(1),jdim,jdim,jdim);
@@ -1079,8 +1094,6 @@ inline
T_INT SNAKokkos<DeviceType>::size_thread_scratch_arrays() {
T_INT size = 0;
int jdim = twojmax + 1;
- size += Kokkos::View<double*, Kokkos::LayoutRight, DeviceType>::shmem_size(ncoeff); // bvec
- size += t_sna_3d::shmem_size(jdim,jdim,jdim); // barray
size += Kokkos::View<double*[3], Kokkos::LayoutRight, DeviceType>::shmem_size(ncoeff); // dbvec
size += t_sna_4d::shmem_size(jdim,jdim,jdim); // dbarray
diff --git a/src/MOLECULE/improper_umbrella.cpp b/src/MOLECULE/improper_umbrella.cpp
index 31d7cba54dca313ae2016fe477b9882e0787f515..8ed3d3a84cd6437a6c0894f9d7140c231234aa75 100644
--- a/src/MOLECULE/improper_umbrella.cpp
+++ b/src/MOLECULE/improper_umbrella.cpp
@@ -189,17 +189,17 @@ void ImproperUmbrella::compute(int eflag, int vflag)
dahy = ary-c*hry;
dahz = arz-c*hrz;
- f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
- f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
- f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
+ f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a;
+ f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a;
+ f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a;
- f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
- f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
- f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
+ f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a;
+ f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a;
+ f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a;
- f4[0] = dahx*rhr;
- f4[1] = dahy*rhr;
- f4[2] = dahz*rhr;
+ f4[0] = dahx*rhr*a;
+ f4[1] = dahy*rhr*a;
+ f4[2] = dahz*rhr*a;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
@@ -208,27 +208,27 @@ void ImproperUmbrella::compute(int eflag, int vflag)
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
- f[i1][0] += f1[0]*a;
- f[i1][1] += f1[1]*a;
- f[i1][2] += f1[2]*a;
+ f[i1][0] += f1[0];
+ f[i1][1] += f1[1];
+ f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
- f[i2][0] += f3[0]*a;
- f[i2][1] += f3[1]*a;
- f[i2][2] += f3[2]*a;
+ f[i2][0] += f3[0];
+ f[i2][1] += f3[1];
+ f[i2][2] += f3[2];
}
if (newton_bond || i3 < nlocal) {
- f[i3][0] += f2[0]*a;
- f[i3][1] += f2[1]*a;
- f[i3][2] += f2[2]*a;
+ f[i3][0] += f2[0];
+ f[i3][1] += f2[1];
+ f[i3][2] += f2[2];
}
if (newton_bond || i4 < nlocal) {
- f[i4][0] += f4[0]*a;
- f[i4][1] += f4[1]*a;
- f[i4][2] += f4[2]*a;
+ f[i4][0] += f4[0];
+ f[i4][1] += f4[1];
+ f[i4][2] += f4[2];
}
if (evflag) {
@@ -247,7 +247,7 @@ void ImproperUmbrella::compute(int eflag, int vflag)
vb3y = x[i4][1] - x[i3][1];
vb3z = x[i4][2] - x[i3][2];
- ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f3,f4,
+ ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f2,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
}
}
diff --git a/src/Makefile b/src/Makefile
index d7b5a9e702d439f9e591364c9561fd9da10fa917..1f0a294e8a71ecb494d885583270db0f8359e5e5 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -64,7 +64,7 @@ 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-CGDNA/README b/src/USER-CGDNA/README
index d71f3b7a43acc9df6f7c56f1077a991ce7e762e0..8e3f16372c99321c631aa98d8efca39c778f6d2e 100644
--- a/src/USER-CGDNA/README
+++ b/src/USER-CGDNA/README
@@ -74,10 +74,10 @@ pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides
pair_oxdna2_excv.cpp, pair_oxdna2_stk.cpp, pair_oxdna2_coaxstk.cpp:
- corresponding pair styles in oxDNA2 (see [3])
+ corresponding pair styles in oxDNA2 (see [3])
pair_oxdna2_dh.cpp: Debye-Hueckel electrostatic interaction between backbone
- sites
+ sites
** Fixes provided by this package:
diff --git a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
index ce5d3a92a9002af04c1e3cbae013bc0c605424a9..f9da40dfb9888e6ccfd12768f202d040a61b5445 100644
--- a/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
+++ b/src/USER-DRUDE/pair_lj_cut_thole_long.cpp
@@ -683,7 +683,7 @@ void *PairLJCutTholeLong::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
- dim = 6;
+ dim = 2;
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
if (strcmp(str,"sigma") == 0) return (void *) sigma;
if (strcmp(str,"scale") == 0) return (void *) scale;
diff --git a/src/USER-DRUDE/pair_thole.cpp b/src/USER-DRUDE/pair_thole.cpp
index 6901ad1f2d6e64ae3686c4eb381730f099d6347d..5a518d819bb9248eebe284a1decd4a1f1678dcdd 100644
--- a/src/USER-DRUDE/pair_thole.cpp
+++ b/src/USER-DRUDE/pair_thole.cpp
@@ -414,7 +414,7 @@ double PairThole::single(int i, int j, int itype, int jtype,
void *PairThole::extract(const char *str, int &dim)
{
- dim = 4;
+ dim = 2;
if (strcmp(str,"scale") == 0) return (void *) scale;
if (strcmp(str,"polar") == 0) return (void *) polar;
if (strcmp(str,"thole") == 0) return (void *) thole;
diff --git a/src/USER-MISC/compute_entropy_atom.cpp b/src/USER-MISC/compute_entropy_atom.cpp
index 4946bc437e7960bba7e9f054d298d191c69f2711..0367d7fe6d9e7605186e79fe0cdac4c05352f2c6 100644
--- a/src/USER-MISC/compute_entropy_atom.cpp
+++ b/src/USER-MISC/compute_entropy_atom.cpp
@@ -65,6 +65,7 @@ ComputeEntropyAtom(LAMMPS *lmp, int narg, char **arg) :
if (cutoff <= 0.0) error->all(FLERR,"Illegal compute entropy/atom"
" command; cutoff must be positive");
+ cutoff2 = 0.;
avg_flag = 0;
local_flag = 0;
@@ -137,15 +138,20 @@ void ComputeEntropyAtom::init()
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute entropy/atom");
- // need a full neighbor list with neighbors of the ghost atoms
-
+ // Request neighbor list
int irequest = neighbor->request(this,instance_me);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 0;
- neighbor->requests[irequest]->ghost = 1;
+ if (avg_flag) {
+ // need a full neighbor list with neighbors of the ghost atoms
+ neighbor->requests[irequest]->ghost = 1;
+ } else {
+ // need a full neighbor list
+ neighbor->requests[irequest]->ghost = 0;
+ }
}
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index d705cba1cabbe3bb1a4b0d39bd724e6d1b629265..b9c357f3635abe9bf81bfcacb64491acb440e6fe 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -58,7 +58,8 @@ static const char cite_fix_bond_react[] =
#define BIG 1.0e20
#define DELTA 16
#define MAXLINE 256
-#define MAXGUESS 20
+#define MAXGUESS 20 // max # of guesses allowed by superimpose algorithm
+#define MAXCONARGS 5 // max # of arguments for any type of constraint
// various statuses of superimpose algorithm:
// ACCEPT: site successfully matched to pre-reacted template
@@ -161,10 +162,15 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(unreacted_mol,nreacts,"bond/react:unreacted_mol");
memory->create(reacted_mol,nreacts,"bond/react:reacted_mol");
memory->create(fraction,nreacts,"bond/react:fraction");
+ memory->create(max_rxn,nreacts,"bond/react:max_rxn");
+ memory->create(nlocalskips,nreacts,"bond/react:nlocalskips");
+ memory->create(nghostlyskips,nreacts,"bond/react:nghostlyskips");
memory->create(seed,nreacts,"bond/react:seed");
memory->create(limit_duration,nreacts,"bond/react:limit_duration");
memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
memory->create(update_edges_flag,nreacts,"bond/react:update_edges_flag");
+ memory->create(nconstraints,nreacts,"bond/react:nconstraints");
+ memory->create(constraints,nreacts,MAXCONARGS,"bond/react:constraints");
memory->create(iatomtype,nreacts,"bond/react:iatomtype");
memory->create(jatomtype,nreacts,"bond/react:jatomtype");
memory->create(ibonding,nreacts,"bond/react:ibonding");
@@ -179,8 +185,10 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
for (int i = 0; i < nreacts; i++) {
fraction[i] = 1;
seed[i] = 12345;
+ max_rxn[i] = INT_MAX;
stabilize_steps_flag[i] = 0;
update_edges_flag[i] = 0;
+ nconstraints[i] = 0;
// set default limit duration to 60 timesteps
limit_duration[i] = 60;
reaction_count[i] = 0;
@@ -244,6 +252,13 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
if (seed[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command: "
"probability seed must be positive");
iarg += 3;
+ } else if (strcmp(arg[iarg],"max_rxn") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
+ "'max_rxn' has too few arguments");
+ max_rxn[rxn] = force->inumeric(FLERR,arg[iarg+1]);
+ if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: "
+ "'max_rxn' cannot be negative");
+ iarg += 2;
} else if (strcmp(arg[iarg],"stabilize_steps") == 0) {
if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword "
"used without stabilization keyword");
@@ -403,6 +418,9 @@ FixBondReact::~FixBondReact()
memory->destroy(reacted_mol);
memory->destroy(fraction);
memory->destroy(seed);
+ memory->destroy(max_rxn);
+ memory->destroy(nlocalskips);
+ memory->destroy(nghostlyskips);
memory->destroy(limit_duration);
memory->destroy(stabilize_steps_flag);
memory->destroy(update_edges_flag);
@@ -674,6 +692,8 @@ void FixBondReact::post_integrate()
reaction_count[i] = 0;
local_rxn_count[i] = 0;
ghostly_rxn_count[i] = 0;
+ nlocalskips[i] = 0;
+ nghostlyskips[i] = 0;
}
if (nevery_check) {
@@ -745,6 +765,7 @@ void FixBondReact::post_integrate()
int j;
for (rxnID = 0; rxnID < nreacts; rxnID++) {
+ if (max_rxn[rxnID] <= reaction_count_total[rxnID]) continue;
for (int ii = 0; ii < nall; ii++) {
partner[ii] = 0;
finalpartner[ii] = 0;
@@ -941,6 +962,7 @@ void FixBondReact::far_partner()
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
+ domain->minimum_image(delx,dely,delz); // ghost location fix
rsq = delx*delx + dely*dely + delz*delz;
if (rsq >= cutsq[rxnID][1] || rsq <= cutsq[rxnID][0]) {
@@ -1122,7 +1144,7 @@ void FixBondReact::superimpose_algorithm()
}
}
- if (status == ACCEPT) { // reaction site found successfully!
+ if (status == ACCEPT && check_constraints()) { // reaction site found successfully!
glove_ghostcheck();
}
hang_catch++;
@@ -1142,14 +1164,43 @@ void FixBondReact::superimpose_algorithm()
MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world);
- for (int i = 0; i < nreacts; i++)
- reaction_count_total[i] += reaction_count[i];
-
- // this assumes compute_vector is called from process 0
- // ...so doesn't bother to bcast ghostly_rxn_count
if (me == 0)
for (int i = 0; i < nreacts; i++)
- reaction_count_total[i] += ghostly_rxn_count[i];
+ reaction_count_total[i] += reaction_count[i] + ghostly_rxn_count[i];
+
+ MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world);
+
+ // check if we overstepped our reaction limit
+ for (int i = 0; i < nreacts; i++) {
+ if (reaction_count_total[i] > max_rxn[i]) {
+ // let's randomly choose rxns to skip, unbiasedly from local and ghostly
+ int local_rxncounts[nprocs];
+ int all_localskips[nprocs];
+ MPI_Gather(&local_rxn_count[i],1,MPI_INT,local_rxncounts,1,MPI_INT,0,world);
+ if (me == 0) {
+ int overstep = reaction_count_total[i] - max_rxn[i];
+ int delta_rxn = reaction_count[i] + ghostly_rxn_count[i];
+ int rxn_by_proc[delta_rxn];
+ for (int j = 0; j < delta_rxn; j++)
+ rxn_by_proc[j] = -1; // corresponds to ghostly
+ int itemp = 0;
+ for (int j = 0; j < nprocs; j++)
+ for (int k = 0; k < local_rxn_count[j]; k++)
+ rxn_by_proc[itemp++] = j;
+ std::random_shuffle(&rxn_by_proc[0],&rxn_by_proc[delta_rxn]);
+ for (int j = 0; j < nprocs; j++)
+ all_localskips[j] = 0;
+ nghostlyskips[i] = 0;
+ for (int j = 0; j < overstep; j++) {
+ if (rxn_by_proc[j] == -1) nghostlyskips[i]++;
+ else all_localskips[rxn_by_proc[j]]++;
+ }
+ }
+ reaction_count_total[i] = max_rxn[i];
+ MPI_Scatter(&all_localskips[0],1,MPI_INT,&nlocalskips[i],1,MPI_INT,0,world);
+ MPI_Bcast(&nghostlyskips[i],1,MPI_INT,0,world);
+ }
+ }
// this updates topology next step
next_reneighbor = update->ntimestep;
@@ -1526,6 +1577,32 @@ void FixBondReact::ring_check()
}
}
+/* ----------------------------------------------------------------------
+evaluate constraints: return 0 if any aren't satisfied
+------------------------------------------------------------------------- */
+
+int FixBondReact::check_constraints()
+{
+ tagint atom1,atom2;
+ double delx,dely,delz,rsq;
+
+ double **x = atom->x;
+
+ for (int i = 0; i < nconstraints[rxnID]; i++) {
+ if (constraints[rxnID][0] == 0) { // 'distance' type
+ atom1 = atom->map(glove[(int) constraints[rxnID][1]-1][1]);
+ atom2 = atom->map(glove[(int) constraints[rxnID][2]-1][1]);
+ delx = x[atom1][0] - x[atom2][0];
+ dely = x[atom1][1] - x[atom2][1];
+ delz = x[atom1][2] - x[atom2][2];
+ domain->minimum_image(delx,dely,delz); // ghost location fix
+ rsq = delx*delx + dely*dely + delz*delz;
+ if (rsq < constraints[rxnID][3] || rsq > constraints[rxnID][4]) return 0;
+ }
+ }
+ return 1;
+}
+
/* ----------------------------------------------------------------------
Get xspecials for current molecule templates
------------------------------------------------------------------------- */
@@ -1945,19 +2022,19 @@ void FixBondReact::glove_ghostcheck()
// 'ghosts of another' indication taken from comm->sendlist
int ghostly = 0;
- if (comm->style == 0) {
- for (int i = 0; i < onemol->natoms; i++) {
- int ilocal = atom->map(glove[i][1]);
- if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
- ghostly = 1;
- break;
+ #if !defined(MPI_STUBS)
+ if (comm->style == 0) {
+ for (int i = 0; i < onemol->natoms; i++) {
+ int ilocal = atom->map(glove[i][1]);
+ if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
+ ghostly = 1;
+ break;
+ }
}
- }
- } else {
- #if !defined(MPI_STUBS)
+ } else {
ghostly = 1;
- #endif
- }
+ }
+ #endif
if (ghostly == 1) {
ghostly_mega_glove[0][ghostly_num_mega] = rxnID;
@@ -2092,18 +2169,26 @@ void FixBondReact::update_everything()
memory->create(update_mega_glove,max_natoms+1,MAX(local_num_mega,global_megasize),"bond/react:update_mega_glove");
for (int pass = 0; pass < 2; pass++) {
-
+ update_num_mega = 0;
+ int iskip[nreacts];
+ for (int i = 0; i < nreacts; i++) iskip[i] = 0;
if (pass == 0) {
- update_num_mega = local_num_mega;
- for (int i = 0; i < update_num_mega; i++) {
+ for (int i = 0; i < local_num_mega; i++) {
+ rxnID = local_mega_glove[0][i];
+ // reactions already shuffled from dedup procedure, so can skip first N
+ if (iskip[rxnID]++ < nlocalskips[rxnID]) continue;
for (int j = 0; j < max_natoms+1; j++)
- update_mega_glove[j][i] = local_mega_glove[j][i];
+ update_mega_glove[j][update_num_mega] = local_mega_glove[j][i];
+ update_num_mega++;
}
} else if (pass == 1) {
- update_num_mega = global_megasize;
for (int i = 0; i < global_megasize; i++) {
+ rxnID = global_mega_glove[0][i];
+ // reactions already shuffled from dedup procedure, so can skip first N
+ if (iskip[rxnID]++ < nghostlyskips[rxnID]) continue;
for (int j = 0; j < max_natoms+1; j++)
- update_mega_glove[j][i] = global_mega_glove[j][i];
+ update_mega_glove[j][update_num_mega] = global_mega_glove[j][i];
+ update_num_mega++;
}
}
@@ -2623,6 +2708,7 @@ void FixBondReact::read(int myrxn)
else if (strstr(line,"equivalences")) sscanf(line,"%d",&nequivalent);
else if (strstr(line,"customIDs")) sscanf(line,"%d",&ncustom);
else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete);
+ else if (strstr(line,"constraints")) sscanf(line,"%d",&nconstraints[myrxn]);
else break;
}
@@ -2654,6 +2740,8 @@ void FixBondReact::read(int myrxn)
CustomEdges(line, myrxn);
} else if (strcmp(keyword,"DeleteIDs") == 0) {
DeleteAtoms(line, myrxn);
+ } else if (strcmp(keyword,"Constraints") == 0) {
+ Constraints(line, myrxn);
} else error->one(FLERR,"Unknown section in superimpose file");
parse_keyword(1,line,keyword);
@@ -2729,6 +2817,27 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn)
}
}
+void FixBondReact::Constraints(char *line, int myrxn)
+{
+ double tmp[MAXCONARGS];
+ int n = strlen("distance") + 1;
+ char *constraint_type = new char[n];
+ for (int i = 0; i < nconstraints[myrxn]; i++) {
+ readline(line);
+ sscanf(line,"%s",constraint_type);
+ if (strcmp(constraint_type,"distance") == 0) {
+ constraints[myrxn][0] = 0; // 0 = 'distance' ...maybe use another enum eventually
+ sscanf(line,"%*s %lg %lg %lg %lg",&tmp[0],&tmp[1],&tmp[2],&tmp[3]);
+ constraints[myrxn][1] = tmp[0];
+ constraints[myrxn][2] = tmp[1];
+ constraints[myrxn][3] = tmp[2]*tmp[2]; // using square of distance
+ constraints[myrxn][4] = tmp[3]*tmp[3];
+ } else
+ error->one(FLERR,"Illegal constraint type in 'Constraints' section of map file");
+ }
+ delete [] constraint_type;
+}
+
void FixBondReact::open(char *file)
{
fp = fopen(file,"r");
diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h
index d6e7b785e7f8662d8d4eca52d5171d3a7a77be3c..74d53b8f21265ff7726ee3971001a64e6de49a11 100644
--- a/src/USER-MISC/fix_bond_react.h
+++ b/src/USER-MISC/fix_bond_react.h
@@ -55,11 +55,14 @@ class FixBondReact : public Fix {
int *iatomtype,*jatomtype;
int *seed;
double **cutsq,*fraction;
+ int *max_rxn,*nlocalskips,*nghostlyskips;
tagint lastcheck;
int stabilization_flag;
int custom_exclude_flag;
int *stabilize_steps_flag;
int *update_edges_flag;
+ int *nconstraints;
+ double **constraints;
int status;
int *groupbits;
@@ -140,6 +143,7 @@ class FixBondReact : public Fix {
void Equivalences(char *,int);
void CustomEdges(char *,int);
void DeleteAtoms(char *,int);
+ void Constraints(char *,int);
void make_a_guess ();
void neighbor_loop();
@@ -147,6 +151,7 @@ class FixBondReact : public Fix {
void crosscheck_the_neighbor();
void inner_crosscheck_loop();
void ring_check();
+ int check_constraints();
void open(char *);
void readline(char *);
diff --git a/src/USER-MISC/improper_fourier.cpp b/src/USER-MISC/improper_fourier.cpp
index 11478d08eab135f70baa9ab6d69a762b4a302672..927478fa1a9245f640e40562d84033001bd2afba 100644
--- a/src/USER-MISC/improper_fourier.cpp
+++ b/src/USER-MISC/improper_fourier.cpp
@@ -206,17 +206,17 @@ void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int
dahy = ary-c*hry;
dahz = arz-c*hrz;
- f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
- f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
- f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
+ f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a;
+ f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a;
+ f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a;
- f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
- f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
- f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
+ f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a;
+ f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a;
+ f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a;
- f4[0] = dahx*rhr;
- f4[1] = dahy*rhr;
- f4[2] = dahz*rhr;
+ f4[0] = dahx*rhr*a;
+ f4[1] = dahy*rhr*a;
+ f4[2] = dahz*rhr*a;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
@@ -225,32 +225,32 @@ void ImproperFourier::addone(const int &i1,const int &i2,const int &i3,const int
// apply force to each of 4 atoms
if (newton_bond || i1 < nlocal) {
- f[i1][0] += f1[0]*a;
- f[i1][1] += f1[1]*a;
- f[i1][2] += f1[2]*a;
+ f[i1][0] += f1[0];
+ f[i1][1] += f1[1];
+ f[i1][2] += f1[2];
}
if (newton_bond || i2 < nlocal) {
- f[i2][0] += f3[0]*a;
- f[i2][1] += f3[1]*a;
- f[i2][2] += f3[2]*a;
+ f[i2][0] += f3[0];
+ f[i2][1] += f3[1];
+ f[i2][2] += f3[2];
}
if (newton_bond || i3 < nlocal) {
- f[i3][0] += f2[0]*a;
- f[i3][1] += f2[1]*a;
- f[i3][2] += f2[2]*a;
+ f[i3][0] += f2[0];
+ f[i3][1] += f2[1];
+ f[i3][2] += f2[2];
}
if (newton_bond || i4 < nlocal) {
- f[i4][0] += f4[0]*a;
- f[i4][1] += f4[1]*a;
- f[i4][2] += f4[2]*a;
+ 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,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
+ ev_tally(i1,i2,i3,i4,nlocal,newton_bond,eimproper,f1,f2,f4,
+ -vb1x,-vb1y,-vb1z,vb2x-vb1x,vb2y-vb1y,vb2z-vb1z,vb3x-vb2x,vb3y-vb2y,vb3z-vb2z);
}
/* ---------------------------------------------------------------------- */
diff --git a/src/USER-NETCDF/dump_netcdf.cpp b/src/USER-NETCDF/dump_netcdf.cpp
index e4c0115793482efc11e54bd784f664bea89293d9..f297ef45eb8a175084d8d31dac499958a078603a 100644
--- a/src/USER-NETCDF/dump_netcdf.cpp
+++ b/src/USER-NETCDF/dump_netcdf.cpp
@@ -281,6 +281,9 @@ void DumpNetCDF::openfile()
// get total number of atoms
ntotalgr = group->count(igroup);
+ for (int i = 0; i < DUMP_NC_MAX_DIMS; i++) {
+ vector_dim[i] = -1;
+ }
if (filewriter) {
if (append_flag && !multifile && access(filecurrent, F_OK) != -1) {
@@ -294,9 +297,6 @@ void DumpNetCDF::openfile()
// dimensions
NCERRX( nc_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR );
- NCERRX( nc_inq_dimid(ncid, NC_SPATIAL_STR, &spatial_dim),
- NC_SPATIAL_STR );
- NCERRX( nc_inq_dimid(ncid, NC_VOIGT_STR, &Voigt_dim), NC_VOIGT_STR );
NCERRX( nc_inq_dimid(ncid, NC_ATOM_STR, &atom_dim), NC_ATOM_STR );
NCERRX( nc_inq_dimid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_dim),
NC_CELL_SPATIAL_STR );
@@ -304,6 +304,26 @@ void DumpNetCDF::openfile()
NC_CELL_ANGULAR_STR );
NCERRX( nc_inq_dimid(ncid, NC_LABEL_STR, &label_dim), NC_LABEL_STR );
+ for (int i = 0; i < n_perat; i++) {
+ int dims = perat[i].dims;
+ if (vector_dim[dims] < 0) {
+ char dimstr[1024];
+ if (dims == 3) {
+ strcpy(dimstr, NC_SPATIAL_STR);
+ }
+ else if (dims == 6) {
+ strcpy(dimstr, NC_VOIGT_STR);
+ }
+ else {
+ sprintf(dimstr, "vec%i", dims);
+ }
+ if (dims != 1) {
+ NCERRX( nc_inq_dimid(ncid, dimstr, &vector_dim[dims]),
+ dimstr );
+ }
+ }
+ }
+
// default variables
NCERRX( nc_inq_varid(ncid, NC_SPATIAL_STR, &spatial_var),
NC_SPATIAL_STR );
@@ -320,7 +340,6 @@ void DumpNetCDF::openfile()
NCERRX( nc_inq_varid(ncid, NC_CELL_ANGLES_STR, &cell_angles_var),
NC_CELL_ANGLES_STR);
- // variables specified in the input file
for (int i = 0; i < n_perat; i++) {
NCERRX( nc_inq_varid(ncid, perat[i].name, &perat[i].var),
perat[i].name );
@@ -359,10 +378,6 @@ void DumpNetCDF::openfile()
// dimensions
NCERRX( nc_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim),
NC_FRAME_STR );
- NCERRX( nc_def_dim(ncid, NC_SPATIAL_STR, 3, &spatial_dim),
- NC_SPATIAL_STR );
- NCERRX( nc_def_dim(ncid, NC_VOIGT_STR, 6, &Voigt_dim),
- NC_VOIGT_STR );
NCERRX( nc_def_dim(ncid, NC_ATOM_STR, ntotalgr, &atom_dim),
NC_ATOM_STR );
NCERRX( nc_def_dim(ncid, NC_CELL_SPATIAL_STR, 3, &cell_spatial_dim),
@@ -372,13 +387,33 @@ void DumpNetCDF::openfile()
NCERRX( nc_def_dim(ncid, NC_LABEL_STR, 10, &label_dim),
NC_LABEL_STR );
+ for (int i = 0; i < n_perat; i++) {
+ int dims = perat[i].dims;
+ if (vector_dim[dims] < 0) {
+ char dimstr[1024];
+ if (dims == 3) {
+ strcpy(dimstr, NC_SPATIAL_STR);
+ }
+ else if (dims == 6) {
+ strcpy(dimstr, NC_VOIGT_STR);
+ }
+ else {
+ sprintf(dimstr, "vec%i", dims);
+ }
+ if (dims != 1) {
+ NCERRX( nc_def_dim(ncid, dimstr, dims, &vector_dim[dims]),
+ dimstr );
+ }
+ }
+ }
+
// default variables
- dims[0] = spatial_dim;
+ dims[0] = vector_dim[3];
NCERRX( nc_def_var(ncid, NC_SPATIAL_STR, NC_CHAR, 1, dims, &spatial_var),
NC_SPATIAL_STR );
NCERRX( nc_def_var(ncid, NC_CELL_SPATIAL_STR, NC_CHAR, 1, dims,
&cell_spatial_var), NC_CELL_SPATIAL_STR );
- dims[0] = spatial_dim;
+ dims[0] = vector_dim[3];
dims[1] = label_dim;
NCERRX( nc_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims,
&cell_angular_var), NC_CELL_ANGULAR_STR );
@@ -400,7 +435,7 @@ void DumpNetCDF::openfile()
// variables specified in the input file
dims[0] = frame_dim;
dims[1] = atom_dim;
- dims[2] = spatial_dim;
+ dims[2] = vector_dim[3];
for (int i = 0; i < n_perat; i++) {
nc_type xtype;
@@ -419,53 +454,27 @@ void DumpNetCDF::openfile()
if (perat[i].constant) {
// this quantity will only be written once
- if (perat[i].dims == 6) {
- // this is a tensor in Voigt notation
- dims[2] = Voigt_dim;
- NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1,
- &perat[i].var), perat[i].name );
- }
- else if (perat[i].dims == 3) {
- // this is a vector, we need to store x-, y- and z-coordinates
- dims[2] = spatial_dim;
- NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1,
- &perat[i].var), perat[i].name );
- }
- else if (perat[i].dims == 1) {
+ if (perat[i].dims == 1) {
NCERRX( nc_def_var(ncid, perat[i].name, xtype, 1, dims+1,
- &perat[i].var), perat[i].name );
+ &perat[i].var), perat[i].name );
}
else {
- char errstr[1024];
- sprintf(errstr, "%i dimensions for '%s'. Not sure how to write "
- "this to the NetCDF trajectory file.", perat[i].dims,
- perat[i].name);
- error->all(FLERR,errstr);
+ // this is a vector
+ dims[1] = vector_dim[perat[i].dims];
+ NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims+1,
+ &perat[i].var), perat[i].name );
}
}
else {
- if (perat[i].dims == 6) {
- // this is a tensor in Voigt notation
- dims[2] = Voigt_dim;
- NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims,
- &perat[i].var), perat[i].name );
- }
- else if (perat[i].dims == 3) {
- // this is a vector, we need to store x-, y- and z-coordinates
- dims[2] = spatial_dim;
- NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims,
- &perat[i].var), perat[i].name );
- }
- else if (perat[i].dims == 1) {
+ if (perat[i].dims == 1) {
NCERRX( nc_def_var(ncid, perat[i].name, xtype, 2, dims,
&perat[i].var), perat[i].name );
}
else {
- char errstr[1024];
- sprintf(errstr, "%i dimensions for '%s'. Not sure how to write "
- "this to the NetCDF trajectory file.", perat[i].dims,
- perat[i].name);
- error->all(FLERR,errstr);
+ // this is a vector
+ dims[2] = vector_dim[perat[i].dims];
+ NCERRX( nc_def_var(ncid, perat[i].name, xtype, 3, dims,
+ &perat[i].var), perat[i].name );
}
}
}
diff --git a/src/USER-NETCDF/dump_netcdf.h b/src/USER-NETCDF/dump_netcdf.h
index f97fd58409fa952ebe44e0bcb97ccd776227d619..f74e95be386fef261c2ad1ad1cce4a615c634446 100644
--- a/src/USER-NETCDF/dump_netcdf.h
+++ b/src/USER-NETCDF/dump_netcdf.h
@@ -72,8 +72,7 @@ class DumpNetCDF : public DumpCustom {
int ncid;
int frame_dim;
- int spatial_dim;
- int Voigt_dim;
+ int vector_dim[DUMP_NC_MAX_DIMS];
int atom_dim;
int cell_spatial_dim;
int cell_angular_dim;
diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.cpp b/src/USER-NETCDF/dump_netcdf_mpiio.cpp
index 733fae10f33d1c536d7ea79e451bb4d856785434..026a6eaa3aadc7c41db1f3b4e70c917e4fa70f8e 100644
--- a/src/USER-NETCDF/dump_netcdf_mpiio.cpp
+++ b/src/USER-NETCDF/dump_netcdf_mpiio.cpp
@@ -278,6 +278,9 @@ void DumpNetCDFMPIIO::openfile()
// get total number of atoms
ntotalgr = group->count(igroup);
+ for (int i = 0; i < DUMP_NC_MPIIO_MAX_DIMS; i++) {
+ vector_dim[i] = -1;
+ }
if (append_flag && !multifile && access(filecurrent, F_OK) != -1) {
// Fixme! Perform checks if dimensions and variables conform with
@@ -294,9 +297,6 @@ void DumpNetCDFMPIIO::openfile()
// dimensions
NCERRX( ncmpi_inq_dimid(ncid, NC_FRAME_STR, &frame_dim), NC_FRAME_STR );
- NCERRX( ncmpi_inq_dimid(ncid, NC_SPATIAL_STR, &spatial_dim),
- NC_SPATIAL_STR );
- NCERRX( ncmpi_inq_dimid(ncid, NC_VOIGT_STR, &Voigt_dim), NC_VOIGT_STR );
NCERRX( ncmpi_inq_dimid(ncid, NC_ATOM_STR, &atom_dim), NC_ATOM_STR );
NCERRX( ncmpi_inq_dimid(ncid, NC_CELL_SPATIAL_STR, &cell_spatial_dim),
NC_CELL_SPATIAL_STR );
@@ -304,6 +304,26 @@ void DumpNetCDFMPIIO::openfile()
NC_CELL_ANGULAR_STR );
NCERRX( ncmpi_inq_dimid(ncid, NC_LABEL_STR, &label_dim), NC_LABEL_STR );
+ for (int i = 0; i < n_perat; i++) {
+ int dims = perat[i].dims;
+ if (vector_dim[dims] < 0) {
+ char dimstr[1024];
+ if (dims == 3) {
+ strcpy(dimstr, NC_SPATIAL_STR);
+ }
+ else if (dims == 6) {
+ strcpy(dimstr, NC_VOIGT_STR);
+ }
+ else {
+ sprintf(dimstr, "vec%i", dims);
+ }
+ if (dims != 1) {
+ NCERRX( ncmpi_inq_dimid(ncid, dimstr, &vector_dim[dims]),
+ dimstr );
+ }
+ }
+ }
+
// default variables
NCERRX( ncmpi_inq_varid(ncid, NC_SPATIAL_STR, &spatial_var),
NC_SPATIAL_STR );
@@ -358,10 +378,6 @@ void DumpNetCDFMPIIO::openfile()
// dimensions
NCERRX( ncmpi_def_dim(ncid, NC_FRAME_STR, NC_UNLIMITED, &frame_dim),
NC_FRAME_STR );
- NCERRX( ncmpi_def_dim(ncid, NC_SPATIAL_STR, 3, &spatial_dim),
- NC_SPATIAL_STR );
- NCERRX( ncmpi_def_dim(ncid, NC_VOIGT_STR, 6, &Voigt_dim),
- NC_VOIGT_STR );
NCERRX( ncmpi_def_dim(ncid, NC_ATOM_STR, ntotalgr, &atom_dim),
NC_ATOM_STR );
NCERRX( ncmpi_def_dim(ncid, NC_CELL_SPATIAL_STR, 3, &cell_spatial_dim),
@@ -371,13 +387,33 @@ void DumpNetCDFMPIIO::openfile()
NCERRX( ncmpi_def_dim(ncid, NC_LABEL_STR, 10, &label_dim),
NC_LABEL_STR );
+ for (int i = 0; i < n_perat; i++) {
+ int dims = perat[i].dims;
+ if (vector_dim[dims] < 0) {
+ char dimstr[1024];
+ if (dims == 3) {
+ strcpy(dimstr, NC_SPATIAL_STR);
+ }
+ else if (dims == 6) {
+ strcpy(dimstr, NC_VOIGT_STR);
+ }
+ else {
+ sprintf(dimstr, "vec%i", dims);
+ }
+ if (dims != 1) {
+ NCERRX( ncmpi_def_dim(ncid, dimstr, dims, &vector_dim[dims]),
+ dimstr );
+ }
+ }
+ }
+
// default variables
- dims[0] = spatial_dim;
+ dims[0] = vector_dim[3];
NCERRX( ncmpi_def_var(ncid, NC_SPATIAL_STR, NC_CHAR, 1, dims, &spatial_var),
NC_SPATIAL_STR );
NCERRX( ncmpi_def_var(ncid, NC_CELL_SPATIAL_STR, NC_CHAR, 1, dims,
&cell_spatial_var), NC_CELL_SPATIAL_STR );
- dims[0] = spatial_dim;
+ dims[0] = vector_dim[3];
dims[1] = label_dim;
NCERRX( ncmpi_def_var(ncid, NC_CELL_ANGULAR_STR, NC_CHAR, 2, dims,
&cell_angular_var), NC_CELL_ANGULAR_STR );
@@ -399,7 +435,7 @@ void DumpNetCDFMPIIO::openfile()
// variables specified in the input file
dims[0] = frame_dim;
dims[1] = atom_dim;
- dims[2] = spatial_dim;
+ dims[2] = vector_dim[3];
for (int i = 0; i < n_perat; i++) {
nc_type xtype;
@@ -416,28 +452,15 @@ void DumpNetCDFMPIIO::openfile()
xtype = NC_FLOAT;
}
- if (perat[i].dims == 6) {
- // this is a tensor in Voigt notation
- dims[2] = Voigt_dim;
- NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 3, dims,
- &perat[i].var), perat[i].name );
- }
- else if (perat[i].dims == 3) {
- // this is a vector, we need to store x-, y- and z-coordinates
- dims[2] = spatial_dim;
- NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 3, dims,
- &perat[i].var), perat[i].name );
- }
- else if (perat[i].dims == 1) {
+ if (perat[i].dims == 1) {
NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 2, dims,
&perat[i].var), perat[i].name );
}
else {
- char errstr[1024];
- sprintf(errstr, "%i dimensions for '%s'. Not sure how to write "
- "this to the NetCDF trajectory file.", perat[i].dims,
- perat[i].name);
- error->all(FLERR,errstr);
+ // this is a vector
+ dims[2] = vector_dim[perat[i].dims];
+ NCERRX( ncmpi_def_var(ncid, perat[i].name, xtype, 3, dims,
+ &perat[i].var), perat[i].name );
}
}
diff --git a/src/USER-NETCDF/dump_netcdf_mpiio.h b/src/USER-NETCDF/dump_netcdf_mpiio.h
index 330fa46c045b8eee761dce3958422f9db41bed1a..98ccb87927605182b4d1ffbbb1f99abe23c0e54e 100644
--- a/src/USER-NETCDF/dump_netcdf_mpiio.h
+++ b/src/USER-NETCDF/dump_netcdf_mpiio.h
@@ -71,8 +71,7 @@ class DumpNetCDFMPIIO : public DumpCustom {
int ncid;
int frame_dim;
- int spatial_dim;
- int Voigt_dim;
+ int vector_dim[DUMP_NC_MPIIO_MAX_DIMS];
int atom_dim;
int cell_spatial_dim;
int cell_angular_dim;
diff --git a/src/USER-OMP/improper_fourier_omp.cpp b/src/USER-OMP/improper_fourier_omp.cpp
index aed04003a5eff70550f4d98830145a7557cc22b5..77dd36b64f62d014bf3335178585bed290794b37 100644
--- a/src/USER-OMP/improper_fourier_omp.cpp
+++ b/src/USER-OMP/improper_fourier_omp.cpp
@@ -239,17 +239,17 @@ void ImproperFourierOMP::add1_thr(const int i1,const int i2,
dahy = ary-c*hry;
dahz = arz-c*hrz;
- f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
- f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
- f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
+ f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a;
+ f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a;
+ f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a;
- f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
- f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
- f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
+ f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a;
+ f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a;
+ f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a;
- f4[0] = dahx*rhr;
- f4[1] = dahy*rhr;
- f4[2] = dahz*rhr;
+ f4[0] = dahx*rhr*a;
+ f4[1] = dahy*rhr*a;
+ f4[2] = dahz*rhr*a;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
@@ -258,30 +258,31 @@ void ImproperFourierOMP::add1_thr(const int i1,const int i2,
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
- f[i1][0] += f1[0]*a;
- f[i1][1] += f1[1]*a;
- f[i1][2] += f1[2]*a;
+ f[i1][0] += f1[0];
+ f[i1][1] += f1[1];
+ f[i1][2] += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
- f[i2][0] += f3[0]*a;
- f[i2][1] += f3[1]*a;
- f[i2][2] += f3[2]*a;
+ f[i2][0] += f3[0];
+ f[i2][1] += f3[1];
+ f[i2][2] += f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
- f[i3][0] += f2[0]*a;
- f[i3][1] += f2[1]*a;
- f[i3][2] += f2[2]*a;
+ f[i3][0] += f2[0];
+ f[i3][1] += f2[1];
+ f[i3][2] += f2[2];
}
if (NEWTON_BOND || i4 < nlocal) {
- f[i4][0] += f4[0]*a;
- f[i4][1] += f4[1]*a;
- f[i4][2] += f4[2]*a;
+ f[i4][0] += f4[0];
+ f[i4][1] += f4[1];
+ f[i4][2] += f4[2];
}
if (EVFLAG)
- ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
- vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
+ ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f2,f4,
+ -vb1x,-vb1y,-vb1z,vb2x-vb1x,vb2y-vb1y,vb2z-vb1z,vb3x-vb2x,vb3y-vb2y,vb3z-vb2z,thr);
+
}
diff --git a/src/USER-OMP/improper_umbrella_omp.cpp b/src/USER-OMP/improper_umbrella_omp.cpp
index dc11f24a4de084b07b666c08b76271d135218115..69d41176c64287c55a3663f4db259df03bd5b319 100644
--- a/src/USER-OMP/improper_umbrella_omp.cpp
+++ b/src/USER-OMP/improper_umbrella_omp.cpp
@@ -212,17 +212,17 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
dahy = ary-c*hry;
dahz = arz-c*hrz;
- f2[0] = (dhay*vb1z - dhaz*vb1y)*rar;
- f2[1] = (dhaz*vb1x - dhax*vb1z)*rar;
- f2[2] = (dhax*vb1y - dhay*vb1x)*rar;
+ f2[0] = (dhay*vb1z - dhaz*vb1y)*rar*a;
+ f2[1] = (dhaz*vb1x - dhax*vb1z)*rar*a;
+ f2[2] = (dhax*vb1y - dhay*vb1x)*rar*a;
- f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar;
- f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar;
- f3[2] = (-dhax*vb2y + dhay*vb2x)*rar;
+ f3[0] = (-dhay*vb2z + dhaz*vb2y)*rar*a;
+ f3[1] = (-dhaz*vb2x + dhax*vb2z)*rar*a;
+ f3[2] = (-dhax*vb2y + dhay*vb2x)*rar*a;
- f4[0] = dahx*rhr;
- f4[1] = dahy*rhr;
- f4[2] = dahz*rhr;
+ f4[0] = dahx*rhr*a;
+ f4[1] = dahy*rhr*a;
+ f4[2] = dahz*rhr*a;
f1[0] = -(f2[0] + f3[0] + f4[0]);
f1[1] = -(f2[1] + f3[1] + f4[1]);
@@ -231,27 +231,27 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
// apply force to each of 4 atoms
if (NEWTON_BOND || i1 < nlocal) {
- f[i1].x += f1[0]*a;
- f[i1].y += f1[1]*a;
- f[i1].z += f1[2]*a;
+ f[i1].x += f1[0];
+ f[i1].y += f1[1];
+ f[i1].z += f1[2];
}
if (NEWTON_BOND || i2 < nlocal) {
- f[i2].x += f3[0]*a;
- f[i2].y += f3[1]*a;
- f[i2].z += f3[2]*a;
+ f[i2].x += f3[0];
+ f[i2].y += f3[1];
+ f[i2].z += f3[2];
}
if (NEWTON_BOND || i3 < nlocal) {
- f[i3].x += f2[0]*a;
- f[i3].y += f2[1]*a;
- f[i3].z += f2[2]*a;
+ f[i3].x += f2[0];
+ f[i3].y += f2[1];
+ f[i3].z += f2[2];
}
if (NEWTON_BOND || i4 < nlocal) {
- f[i4].x += f4[0]*a;
- f[i4].y += f4[1]*a;
- f[i4].z += f4[2]*a;
+ f[i4].x += f4[0];
+ f[i4].y += f4[1];
+ f[i4].z += f4[2];
}
if (EVFLAG) {
@@ -270,7 +270,7 @@ void ImproperUmbrellaOMP::eval(int nfrom, int nto, ThrData * const thr)
vb3y = x[i4].y - x[i3].y;
vb3z = x[i4].z - x[i3].z;
- ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f3,f4,
+ ev_tally_thr(this,i1,i2,i3,i4,nlocal,NEWTON_BOND,eimproper,f1,f2,f4,
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,thr);
}
}
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..f8346f1e33094e38ee11b16b82e89d0f69cc7892
--- /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] = 0.5*(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 / (2.0*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(2.0*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.
+
+*/
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index 9c536dcbc6610478c57bf05a5e4e913130b73db3..c3d55d76a41c8b0e53dc0e45598f2a611eab65c4 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -725,6 +725,24 @@ void CreateAtoms::add_lattice()
domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxhi[2],
xmin,ymin,zmin,xmax,ymax,zmax);
+ // narrow down min/max further by extent of the region, if possible
+
+ if (domain->regions[nregion]->bboxflag) {
+ const double rxmin = domain->regions[nregion]->extent_xlo;
+ const double rxmax = domain->regions[nregion]->extent_xhi;
+ const double rymin = domain->regions[nregion]->extent_ylo;
+ const double rymax = domain->regions[nregion]->extent_yhi;
+ const double rzmin = domain->regions[nregion]->extent_zlo;
+ const double rzmax = domain->regions[nregion]->extent_zhi;
+
+ if (rxmin > xmin) xmin = (rxmin > xmax) ? xmax : rxmin;
+ if (rxmax < xmax) xmax = (rxmax < xmin) ? xmin : rxmax;
+ if (rymin > ymin) ymin = (rymin > ymax) ? ymax : rymin;
+ if (rymax < ymax) ymax = (rymax < ymin) ? ymin : rymax;
+ if (rzmin > zmin) zmin = (rzmin > zmax) ? zmax : rzmin;
+ if (rzmax < zmax) zmax = (rzmax < zmin) ? zmin : rzmax;
+ }
+
// ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox
// overlap = any part of a unit cell (face,edge,pt) in common with my subbox
// in lattice space, subbox is a tilted box
@@ -751,15 +769,32 @@ void CreateAtoms::add_lattice()
// convert lattice coords to box coords
// add atom or molecule (on each basis point) if it meets all criteria
- double **basis = domain->lattice->basis;
- double x[3],lamda[3];
- double *coord;
+ const double * const * const basis = domain->lattice->basis;
+
+ // rough estimate of total time used for create atoms.
+ // one inner loop takes about 25ns on a typical desktop CPU core in 2019
+ double testimate = 2.5e-8/3600.0; // convert seconds to hours
+ testimate *= static_cast<double>(khi-klo+1);
+ testimate *= static_cast<double>(jhi-jlo+1);
+ testimate *= static_cast<double>(ihi-ilo+1);
+ testimate *= static_cast<double>(nbasis);
+ double maxestimate = 0.0;
+ MPI_Reduce(&testimate,&maxestimate,1,MPI_DOUBLE,MPI_MAX,0,world);
+
+ if ((comm->me == 0) && (maxestimate > 0.01)) {
+ if (screen) fprintf(screen,"WARNING: create_atoms will take "
+ "approx. %.2f hours to complete\n",maxestimate);
+ if (logfile) fprintf(logfile,"WARNING: create_atoms will take "
+ "approx. %.2f hours to complete\n",maxestimate);
+ }
int i,j,k,m;
- for (k = klo; k <= khi; k++)
- for (j = jlo; j <= jhi; j++)
- for (i = ilo; i <= ihi; i++)
+ for (k = klo; k <= khi; k++) {
+ for (j = jlo; j <= jhi; j++) {
+ for (i = ilo; i <= ihi; i++) {
for (m = 0; m < nbasis; m++) {
+ double *coord;
+ double x[3],lamda[3];
x[0] = i + basis[m][0];
x[1] = j + basis[m][1];
@@ -794,8 +829,12 @@ void CreateAtoms::add_lattice()
if (mode == ATOM) atom->avec->create_atom(basistype[m],x);
else add_molecule(x);
}
+ }
+ }
+ }
}
+
/* ----------------------------------------------------------------------
add a randomly rotated molecule with its center at center
if quat_user set, perform requested rotation