From c5db3ff401260e0277c190329df6c7cfb1caabf5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 12 May 2017 23:27:58 -0400 Subject: [PATCH 1/6] two small doc corrections from Andrew Jewett for pair style gauss and dihedral style spherical --- doc/src/dihedral_spherical.txt | 17 +++++++++-------- doc/src/pair_gauss.txt | 2 +- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt index 3f888db01b..c71a319912 100644 --- a/doc/src/dihedral_spherical.txt +++ b/doc/src/dihedral_spherical.txt @@ -14,10 +14,10 @@ dihedral_style spherical :pre [Examples:] -dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 -dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 & - 17.3 0 0.0 0 1 158 1 0 0.0 0 & - 15.1 0 0.0 0 0 0.0 0 1 167.3 1 :pre +dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 +dihedral_coeff 1 3 69.3 1 93.9 1 1 90 0 1 90 0 & + 49.1 0 0.00 0 1 74.4 1 0 0.00 0 & + 25.2 0 0.00 0 0 0.00 0 1 48.1 1 [Description:] @@ -35,13 +35,14 @@ the dihedral interaction even if it requires adding additional terms to the expansion (as was done in the second example). A careful choice of parameters can prevent singularities that occur with traditional force-fields whenever theta1 or theta2 approach 0 or 180 degrees. + The last example above corresponds to an interaction with a single energy -minima located at phi=114, theta1=158, theta2=167.3 degrees, and it remains +minima located near phi=93.9, theta1=74.4, theta2=48.1 degrees, and it remains numerically stable at all angles (phi, theta1, theta2). In this example, -the coefficients 17.3, and 15.1 can be physically interpreted as the +the coefficients 49.1, and 25.2 can be physically interpreted as the harmonic spring constants for theta1 and theta2 around their minima. -The coefficient 286.1 is the harmonic spring constant for phi after -division by sin(158)*sin(167.3) (the minima positions for theta1 and theta2). +The coefficient 69.3 is the harmonic spring constant for phi after +division by sin(74.4)*sin(48.1) (the minima positions for theta1 and theta2). The following coefficients must be defined for each dihedral type via the "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt index 92d8b51d8b..f6f46a2de8 100644 --- a/doc/src/pair_gauss.txt +++ b/doc/src/pair_gauss.txt @@ -128,7 +128,7 @@ The B parameter is converted to a distance (sigma), before mixing afterwards (using B=sigma^2). Negative A values are converted to positive A values (using abs(A)) before mixing, and converted back after mixing -(by multiplying by sign(Ai)*sign(Aj)). +(by multiplying by min(sign(Ai),sign(Aj))). This way, if either particle is repulsive (if Ai<0 or Aj<0), then the default interaction between both particles will be repulsive. From d807ba1974d548515a2af77c340871c45663b920 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 16 May 2017 00:26:39 -0400 Subject: [PATCH 2/6] whitespace cleanup --- src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp index af19f3eb3b..1e34b06478 100644 --- a/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp +++ b/src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp @@ -393,10 +393,10 @@ void PairLJCharmmfswCoulCharmmfsh::write_restart(FILE *fp) 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(&eps14[i][j],sizeof(double),1,fp); - fwrite(&sigma14[i][j],sizeof(double),1,fp); + fwrite(&epsilon[i][j],sizeof(double),1,fp); + fwrite(&sigma[i][j],sizeof(double),1,fp); + fwrite(&eps14[i][j],sizeof(double),1,fp); + fwrite(&sigma14[i][j],sizeof(double),1,fp); } } } From 66084ad1f41adf9067bcf6c09f3ee0c2deef74b6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 16 May 2017 04:27:15 -0400 Subject: [PATCH 3/6] fix typo in rerun docs. closes #486 --- doc/src/rerun.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt index 860ee68033..edf94cc711 100644 --- a/doc/src/rerun.txt +++ b/doc/src/rerun.txt @@ -15,7 +15,7 @@ rerun file1 file2 ... keyword args ... :pre file1,file2,... = dump file(s) to read :ulb,l one or more keywords may be appended, keyword {dump} must appear and be last :l keyword = {first} or {last} or {every} or {skip} or {start} or {stop} or {dump} - {first} args = Nfirts + {first} args = Nfirst Nfirst = dump timestep to start on {last} args = Nlast Nlast = dumptimestep to stop on From 597f95fb1b29a6e73e8e36533abdecc26ab51280 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 16 May 2017 17:53:12 -0400 Subject: [PATCH 4/6] fix duplicate reference --- doc/src/pair_meam_spline.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index e4d86521c9..2295a6640b 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -33,7 +33,7 @@ atoms J, I, and K centered on atom I. The five functions Phi, U, rho, f, and g are represented by cubic splines. The {meam/spline} style also supports a new style multicomponent -modified embedded-atom method (MEAM) potential "(Zhang)"_#Zhang1, where +modified embedded-atom method (MEAM) potential "(Zhang)"_#Zhang4, where the total energy E is given by :c,image(Eqs/pair_meam_spline_multicomponent.jpg) @@ -164,5 +164,5 @@ for more info. Kress, Modelling Simulation Materials Science Engineering, 8, 825 (2000). -:link(Zhang1) +:link(Zhang4) [(Zhang)] Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016). From 085f3afdfb089a85bd0958fb6436f15c1463c5e2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 May 2017 09:59:30 -0400 Subject: [PATCH 5/6] fix typo in docs --- doc/src/velocity.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/velocity.txt b/doc/src/velocity.txt index 70ddb559fa..b8299a5acf 100644 --- a/doc/src/velocity.txt +++ b/doc/src/velocity.txt @@ -61,7 +61,7 @@ keyword/value parameters. Not all options are used by each style. Each option has a default as listed below. The {create} style generates an ensemble of velocities using a random -number generator with the specified seed as the specified temperature. +number generator with the specified seed at the specified temperature. The {set} style sets the velocities of all atoms in the group to the specified values. If any component is specified as NULL, then it is From bd11479a16880c55e89dcc8ee65b886f8baf9eb5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 18 May 2017 00:50:35 -0400 Subject: [PATCH 6/6] lock the sphinx command to version 1.5.6, since version 1.6.x seems to break one of the extensions we use --- doc/Makefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/Makefile b/doc/Makefile index fd087f0344..a1f76d7041 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -158,7 +158,7 @@ $(VENV): @( \ virtualenv -p $(PYTHON) $(VENV); \ . $(VENV)/bin/activate; \ - pip install Sphinx; \ + pip install Sphinx==1.5.6; \ pip install sphinxcontrib-images; \ deactivate;\ )