diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
new file mode 100644
index 0000000000000000000000000000000000000000..fdee6325d0f65c04fa76eec1cfa58ee90012c8c9
--- /dev/null
+++ b/.github/CODEOWNERS
@@ -0,0 +1,21 @@
+# This file contains file patterns that triggers automatic
+# code review requests from users that are owners of these files
+# Order matters, the last match has the highest precedence
+
+# library folders
+lib/colvars/* @giacomofiorin
+lib/compress/* @akohlmey
+lib/kokkos/* @stanmoore1
+lib/molfile/* @akohlmey
+lib/qmmm/* @akohlmey
+lib/vtk/* @rbberger
+
+# packages
+src/KOKKOS @stanmoore1
+src/USER-CGSDK @akohlmey
+src/USER-COLVARS @giacomofiorin
+src/USER-OMP @akohlmey
+src/USER-QMMM @akohlmey
+
+# tools
+tools/msi2lmp/* @akohlmey
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index 86d690ccbd2c586617cda802ef445ba638623228..a840c2e0c68cb823b0ed3948a4328e09501cfe9b 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -79,7 +79,7 @@ bug reports and feature requests are mainly coordinated through the
"LAMMPS project on GitHub."_https://github.com/lammps/lammps
The lammps.org domain, currently hosting "public continuous integration
testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux
-RPM and Windows installer packages"_http://rpm.lammps.org is located
+RPM and Windows installer packages"_http://packages.lammps.org is located
at Temple University and managed by Richard Berger,
richard.berger at temple.edu.
diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt
index 408c01d52cf2dcbcee7fb1242dc01b74e2752734..f5829f92fb35119d352a1ddd5305b2471e17b9d5 100644
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@@ -7886,8 +7886,8 @@ keyword to allow for additional bonds to be formed :dd
{New bond exceeded special list size in fix bond/create} :dt
-See the "special_bonds extra" command
-(or the "read_data extra/special/per/atom" command)
+See the "read_data extra/special/per/atom" command
+(or the "create_box extra/special/per/atom" command)
for info on how to leave space in the special bonds
list to allow for additional bonds to be formed. :dd
@@ -9666,8 +9666,8 @@ you are running. :dd
{Special list size exceeded in fix bond/create} :dt
-See the special_bonds extra command
-(or the read_data extra/special/per/atom command)
+See the "read_data extra/special/per/atom" command
+(or the "create_box extra/special/per/atom" command)
for info on how to leave space in the special bonds
list to allow for additional bonds to be formed. :dd
diff --git a/doc/src/Section_start.txt b/doc/src/Section_start.txt
index 6eef155be2db41542603ece8b50bb4aea5e7a28d..a25ec11cfe8507a989e3f453f5433d362f92484f 100644
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@@ -662,27 +662,25 @@ your own build system. Due to differences between the Windows OS
and Windows system libraries to Unix-like environments like Linux
or MacOS, when compiling for Windows a few adjustments may be needed:
-Do not set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable)
+Do [not] set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable)
Add -lwsock32 -lpsapi to the linker flags (see LIB makefile variable)
-Try adding -static-libgcc or -static or both to the linker flags when your
-LAMMPS executable complains about missing .dll files :ul
+Try adding -static-libgcc or -static or both to the linker flags when your LAMMPS executable complains about missing .dll files :ul
-Since none of the current LAMMPS core developers
-has significant experience building executables on Windows, we are
-happy to distribute contributed instructions and modifications, but
-we cannot provide support for those.
+Since none of the current LAMMPS core developers has significant
+experience building executables on Windows, we are happy to distribute
+contributed instructions and modifications to improve the situation,
+but we cannot provide support for those.
With the so-called "Anniversary Update" to Windows 10, there is a
Ubuntu Linux subsystem available for Windows, that can be installed
and then used to compile/install LAMMPS as if you are running on a
Ubuntu Linux system instead of Windows.
-As an alternative, you can download "daily builds" (and some older
-versions) of the installer packages from
-"rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html.
-These executables are built with most optional packages and the
-download includes documentation, potential files, some tools and
-many examples, but no source code.
+As an alternative, you can download pre-compiled installer packages from
+"packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html.
+These executables are built with most optional packages included and the
+download includes documentation, potential files, some tools and many
+examples, but no source code.
:line
@@ -1095,7 +1093,7 @@ LAMMPS to be built with one or more of its optional packages.
:line
On a Windows box, you can skip making LAMMPS and simply download an
-installer package from "here"_http://rpm.lammps.org/windows.html
+installer package from "here"_http://packages.lammps.org/windows.html
For running the non-MPI executable, follow these steps:
@@ -1107,18 +1105,27 @@ the [in.lj] input from the bench folder. (e.g. by typing: cd "Documents"). :l
At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj]
with the name of your LAMMPS input script. :l
+
+The serial executable includes support for multi-threading
+parallelization from the styles in the USER-OMP packages.
+
+To run with, e.g. 4 threads, type "lmp_serial -in in.lj -pk omp 4 -sf omp"
:ule
-For the MPI version, which allows you to run LAMMPS under Windows on
-multiple processors, follow these steps:
+For the MPI version, which allows you to run LAMMPS under Windows with
+the more general message passing parallel library (LAMMPS has been
+designed from ground up to use MPI efficiently), follow these steps:
-Download and install
-"MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads
-for Windows. :ulb,l
+Download and install a compatible MPI library binary package:
+for 32-bit Windows
+"mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
+and for 64-bit Windows
+"mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi
+:ulb,l
The LAMMPS Windows installer packages will automatically adjust your
path for the default location of this MPI package. After the installation
-of the MPICH software, it needs to be integrated into the system.
+of the MPICH2 software, it needs to be integrated into the system.
For this you need to start a Command Prompt in {Administrator Mode}
(right click on the icon and select it). Change into the MPICH2
installation directory, then into the subdirectory [bin] and execute
@@ -1137,7 +1144,7 @@ or
mpiexec -np 4 lmp_mpi -in in.lj :pre
-replacing in.lj with the name of your LAMMPS input script. For the latter
+replacing [in.lj] with the name of your LAMMPS input script. For the latter
case, you may be prompted to enter your password. :l
In this mode, output may not immediately show up on the screen, so if
@@ -1149,6 +1156,11 @@ something like:
lmp_mpi -in in.lj :pre
+And the parallel executable also includes OpenMP multi-threading, which
+can be combined with MPI using something like:
+
+mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre
+
:ule
:line
diff --git a/doc/src/fix_bond_create.txt b/doc/src/fix_bond_create.txt
index a44c3103ddd10489fe639b85e42168d5749c57c3..c0045ac0f081e4df37c9fd6cf201d43238aea88f 100644
--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
@@ -150,10 +150,9 @@ atoms. Note that adding a single bond always adds a new 1st neighbor
but may also induce *many* new 2nd and 3rd neighbors, depending on the
molecular topology of your system. The "extra special per atom"
parameter must typically be set to allow for the new maximum total
-size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3
+size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 2
ways to do this. See the "read_data"_read_data.html or
-"create_box"_create_box.html or "special_bonds extra" commands for
-details.
+"create_box"_create_box.html commands for details.
NOTE: Even if you do not use the {atype}, {dtype}, or {itype}
keywords, the list of topological neighbors is updated for atoms
diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt
index 6a661015bda73c2837da23095afe3c567f37d330..1021c4856b02cc7cb91901d429eb8c1fc2ca22c4 100644
--- a/doc/src/special_bonds.txt
+++ b/doc/src/special_bonds.txt
@@ -25,9 +25,7 @@ keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {c
{coul} values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
{angle} value = {yes} or {no}
- {dihedral} value = {yes} or {no}
- {extra} value = N
- N = number of extra 1-2,1-3,1-4 interactions to save space for :pre
+ {dihedral} value = {yes} or {no} :pre
:ule
Examples:
@@ -36,8 +34,7 @@ special_bonds amber
special_bonds charmm
special_bonds fene dihedral no
special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
-special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
-special_bonds lj/coul 0 1 1 extra 2 :pre
+special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes :pre
[Description:]
@@ -178,14 +175,6 @@ interaction between atoms 2 and 5 will be unaffected (full weighting
of 1.0). If the {dihedral} keyword is specified as {no} which is the
default, then the 2,5 interaction will also be weighted by 0.5.
-The {extra} keyword can be used when additional bonds will be created
-during a simulation run, e.g. by the "fix
-bond/create"_fix_bond_create.html command. It can also be used if
-molecules will be added to the system, e.g. via the "fix
-deposit"_fix_deposit.html, or "fix pour"_fix_pour.html commands, which
-will have atoms with more special neighbors than any atom in the
-current system has.
-
:line
NOTE: LAMMPS stores and maintains a data structure with a list of the
@@ -194,8 +183,9 @@ the system). If new bonds are created (or molecules added containing
atoms with more special neighbors), the size of this list needs to
grow. Note that adding a single bond always adds a new 1st neighbor
but may also induce *many* new 2nd and 3rd neighbors, depending on the
-molecular topology of your system. Using the {extra} keyword leaves
-empty space in the list for this N additional 1st, 2nd, or 3rd
+molecular topology of your system. Using the {extra/special/per/atom}
+keyword to either "read_data"_read_data.html or "create_box"_create_box.html
+reserves empty space in the list for this N additional 1st, 2nd, or 3rd
neighbors to be added. If you do not do this, you may get an error
when bonds (or molecules) are added.
@@ -203,8 +193,7 @@ when bonds (or molecules) are added.
NOTE: If you reuse this command in an input script, you should set all
the options you need each time. This command cannot be used a 2nd
-time incrementally, e.g. to add some extra storage locations via the
-{extra} keyword. E.g. these two commands:
+time incrementally. E.g. these two commands:
special_bonds lj 0.0 1.0 1.0
special_bonds coul 0.0 0.0 1.0
@@ -221,25 +210,6 @@ Coul: coul 0.0 0.0 1.0
because the LJ settings are reset to their default values
each time the command is issued.
-Likewise
-
-special_bonds amber
-special_bonds extra 2 :pre
-
-is not the same as this single command:
-
-special_bonds amber extra 2 :pre
-
-since in the former case, the 2nd command will reset all the LJ and
-Coulombic weights to 0.0 (the default).
-
-One exception to this rule is the {extra} option itself. It is not
-reset to its default value of 0 each time the special_bonds command is
-invoked. This is because it can also be set by the
-"read_data"_read_data.html and "create_box"_create_box.html commands,
-so this command will not override those settings unless you explicitly
-use {extra} as an option.
-
[Restrictions:] none
[Related commands:]
diff --git a/doc/src/tutorial_bash_on_windows.txt b/doc/src/tutorial_bash_on_windows.txt
old mode 100755
new mode 100644
diff --git a/doc/src/tutorial_drude.txt b/doc/src/tutorial_drude.txt
index b9a167b80412e450c8e5f56a412603cfee97aeb1..f6e7eed40bd84cde46e30213c0a14c22244eae86 100644
--- a/doc/src/tutorial_drude.txt
+++ b/doc/src/tutorial_drude.txt
@@ -176,12 +176,13 @@ By recognizing the fix {drude}, LAMMPS will find and store matching
DC-DP pairs and will treat DP as equivalent to their DC in the
{special bonds} relations. It may be necessary to extend the space
for storing such special relations. In this case extra space should
-be reserved by using the {extra} keyword of the {special_bonds}
+be reserved by using the {extra/special/per/atom} keyword of either
+the "read_data"_read_data.html or "create_box"_create_box.html
command. With our phenol, there is 1 more special neighbor for which
space is required. Otherwise LAMMPS crashes and gives the required
value.
-special_bonds lj/coul 0.0 0.0 0.5 extra 1 :pre
+read_data data-p.lmp extra/special/per/atom 1 :pre
Let us assume we want to run a simple NVT simulation at 300 K. Note
that Drude oscillators need to be thermalized at a low temperature in
diff --git a/doc/src/tutorials.txt b/doc/src/tutorials.txt
old mode 100755
new mode 100644
diff --git a/src/force.cpp b/src/force.cpp
index 33e66304067d8c1257d486ed4df44bdf8c80b445..060cae10eb4f9c85e6cfdec200ce069fa10c850f 100644
--- a/src/force.cpp
+++ b/src/force.cpp
@@ -833,10 +833,6 @@ void Force::set_special(int narg, char **arg)
else if (strcmp(arg[iarg+1],"yes") == 0) special_dihedral = 1;
else error->all(FLERR,"Illegal special_bonds command");
iarg += 2;
- } else if (strcmp(arg[iarg],"extra") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal special_bonds command");
- special_extra = atoi(arg[iarg+1]);
- iarg += 2;
} else error->all(FLERR,"Illegal special_bonds command");
}
@@ -844,8 +840,6 @@ void Force::set_special(int narg, char **arg)
if (special_lj[i] < 0.0 || special_lj[i] > 1.0 ||
special_coul[i] < 0.0 || special_coul[i] > 1.0)
error->all(FLERR,"Illegal special_bonds command");
-
- if (special_extra < 0) error->all(FLERR,"Illegal special_bonds command");
}
/* ----------------------------------------------------------------------
diff --git a/src/info.cpp b/src/info.cpp
index 9fcc24fde9ca1e757501ea3acf99c33f1f5a9a10..03eb1e10ed5a6c865473d4ec5d9d7e984a502e8a 100644
--- a/src/info.cpp
+++ b/src/info.cpp
@@ -45,7 +45,7 @@
#include <algorithm>
#ifdef _WIN32
-#define PSAPI_VERSION=1
+#define PSAPI_VERSION 1
#include <windows.h>
#include <stdint.h>
#include <psapi.h>
diff --git a/src/input.cpp b/src/input.cpp
index 570560373a6b219d6c16f090b45f40cf7997ac4a..7d11b8741b976ba47678b8742ded9f1e06ef8bdd 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -1867,7 +1867,6 @@ void Input::special_bonds()
double coul3 = force->special_coul[3];
int angle = force->special_angle;
int dihedral = force->special_dihedral;
- int extra = force->special_extra;
force->set_special(narg,arg);
@@ -1877,8 +1876,7 @@ void Input::special_bonds()
if (lj2 != force->special_lj[2] || lj3 != force->special_lj[3] ||
coul2 != force->special_coul[2] || coul3 != force->special_coul[3] ||
angle != force->special_angle ||
- dihedral != force->special_dihedral ||
- extra != force->special_extra) {
+ dihedral != force->special_dihedral) {
Special special(lmp);
special.build();
}
diff --git a/src/molecule.cpp b/src/molecule.cpp
index e0e9ec8aaf1cb3925a3318fa872edfc82b733e62..b0fec4bcbccdf828f223b0fdb1008c40034ef1e4 100644
--- a/src/molecule.cpp
+++ b/src/molecule.cpp
@@ -427,47 +427,61 @@ void Molecule::read(int flag)
// search line for header keywords and set corresponding variable
- if (strstr(line,"atoms")) sscanf(line,"%d",&natoms);
- else if (strstr(line,"bonds")) sscanf(line,"%d",&nbonds);
- else if (strstr(line,"angles")) sscanf(line,"%d",&nangles);
- else if (strstr(line,"dihedrals")) sscanf(line,"%d",&ndihedrals);
- else if (strstr(line,"impropers")) sscanf(line,"%d",&nimpropers);
-
- else if (strstr(line,"mass")) {
+ int nmatch = 0;
+ int nwant = 0;
+ if (strstr(line,"atoms")) {
+ nmatch = sscanf(line,"%d",&natoms);
+ nwant = 1;
+ } else if (strstr(line,"bonds")) {
+ nmatch = sscanf(line,"%d",&nbonds);
+ nwant = 1;
+ } else if (strstr(line,"angles")) {
+ nmatch = sscanf(line,"%d",&nangles);
+ nwant = 1;
+ } else if (strstr(line,"dihedrals")) {
+ nmatch = sscanf(line,"%d",&ndihedrals);
+ nwant = 1;
+ } else if (strstr(line,"impropers")) {
+ nmatch = sscanf(line,"%d",&nimpropers);
+ nwant = 1;
+ } else if (strstr(line,"mass")) {
massflag = 1;
- sscanf(line,"%lg",&masstotal);
+ nmatch = sscanf(line,"%lg",&masstotal);
+ nwant = 1;
masstotal *= sizescale*sizescale*sizescale;
- }
- else if (strstr(line,"com")) {
+ } else if (strstr(line,"com")) {
comflag = 1;
- sscanf(line,"%lg %lg %lg",&com[0],&com[1],&com[2]);
+ nmatch = sscanf(line,"%lg %lg %lg",&com[0],&com[1],&com[2]);
+ nwant = 3;
com[0] *= sizescale;
com[1] *= sizescale;
com[2] *= sizescale;
if (domain->dimension == 2 && com[2] != 0.0)
error->all(FLERR,"Molecule file z center-of-mass must be 0.0 for 2d");
- }
- else if (strstr(line,"inertia")) {
+ } else if (strstr(line,"inertia")) {
inertiaflag = 1;
- sscanf(line,"%lg %lg %lg %lg %lg %lg",
- &itensor[0],&itensor[1],&itensor[2],
- &itensor[3],&itensor[4],&itensor[5]);
- itensor[0] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- itensor[1] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- itensor[2] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- itensor[3] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- itensor[4] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- itensor[5] *= sizescale*sizescale*sizescale*sizescale*sizescale;
- }
- else if (strstr(line,"body")) {
+ nmatch = sscanf(line,"%lg %lg %lg %lg %lg %lg",
+ &itensor[0],&itensor[1],&itensor[2],
+ &itensor[3],&itensor[4],&itensor[5]);
+ nwant = 6;
+ const double scale5 = sizescale*sizescale*sizescale*sizescale*sizescale;
+ itensor[0] *= scale5;
+ itensor[1] *= scale5;
+ itensor[2] *= scale5;
+ itensor[3] *= scale5;
+ itensor[4] *= scale5;
+ itensor[5] *= scale5;
+ } else if (strstr(line,"body")) {
bodyflag = 1;
avec_body = (AtomVecBody *) atom->style_match("body");
if (!avec_body)
error->all(FLERR,"Molecule file requires atom style body");
- sscanf(line,"%d %d",&nibody,&ndbody);
- }
+ nmatch = sscanf(line,"%d %d",&nibody,&ndbody);
+ nwant = 2;
+ } else break;
- else break;
+ if (nmatch != nwant)
+ error->all(FLERR,"Invalid header in molecule file");
}
// error checks
@@ -493,7 +507,7 @@ void Molecule::read(int flag)
// loop over sections of molecule file
- while (strlen(keyword)) {
+ while (strlen(keyword) > 0) {
if (strcmp(keyword,"Coords") == 0) {
xflag = 1;
if (flag) coords(line);
@@ -517,22 +531,22 @@ void Molecule::read(int flag)
} else if (strcmp(keyword,"Bonds") == 0) {
if (nbonds == 0)
- error->all(FLERR,"Molecule file has bonds but no nbonds setting");
+ error->all(FLERR,"Molecule file has bonds but no nbonds setting");
bondflag = tag_require = 1;
bonds(flag,line);
} else if (strcmp(keyword,"Angles") == 0) {
if (nangles == 0)
- error->all(FLERR,"Molecule file has angles but no nangles setting");
+ error->all(FLERR,"Molecule file has angles but no nangles setting");
angleflag = tag_require = 1;
angles(flag,line);
} else if (strcmp(keyword,"Dihedrals") == 0) {
if (ndihedrals == 0) error->all(FLERR,"Molecule file has dihedrals "
- "but no ndihedrals setting");
+ "but no ndihedrals setting");
dihedralflag = tag_require = 1;
dihedrals(flag,line);
} else if (strcmp(keyword,"Impropers") == 0) {
if (nimpropers == 0) error->all(FLERR,"Molecule file has impropers "
- "but no nimpropers setting");
+ "but no nimpropers setting");
improperflag = tag_require = 1;
impropers(flag,line);
@@ -552,26 +566,26 @@ void Molecule::read(int flag)
shakeatomflag = tag_require = 1;
if (shaketypeflag) shakeflag = 1;
if (!shakeflagflag)
- error->all(FLERR,"Molecule file shake flags not before shake atoms");
+ error->all(FLERR,"Molecule file shake flags not before shake atoms");
if (flag) shakeatom_read(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Shake Bond Types") == 0) {
shaketypeflag = 1;
if (shakeatomflag) shakeflag = 1;
if (!shakeflagflag)
- error->all(FLERR,"Molecule file shake flags not before shake bonds");
+ error->all(FLERR,"Molecule file shake flags not before shake bonds");
if (flag) shaketype_read(line);
else skip_lines(natoms,line);
} else if (strcmp(keyword,"Body Integers") == 0) {
if (bodyflag == 0 || nibody == 0)
- error->all(FLERR,"Molecule file has body params "
+ error->all(FLERR,"Molecule file has body params "
"but no setting for them");
ibodyflag = 1;
body(flag,0,line);
} else if (strcmp(keyword,"Body Doubles") == 0) {
if (bodyflag == 0 || ndbody == 0)
- error->all(FLERR,"Molecule file has body params "
+ error->all(FLERR,"Molecule file has body params "
"but no setting for them");
dbodyflag = 1;
body(flag,1,line);
@@ -618,7 +632,7 @@ void Molecule::read(int flag)
// body particle must have natom = 1
// set radius by having body class compute its own radius
-
+
if (bodyflag) {
radiusflag = 1;
if (natoms != 1)
@@ -641,12 +655,9 @@ void Molecule::coords(char *line)
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 4)
- error->all(FLERR,"Invalid Coords section in molecule file");
- }
- sscanf(line,"%d %lg %lg %lg",&tmp,&x[i][0],&x[i][1],&x[i][2]);
+ if (4 != sscanf(line,"%d %lg %lg %lg",&tmp,&x[i][0],&x[i][1],&x[i][2]))
+ error->all(FLERR,"Invalid Coords section in molecule file");
+
x[i][0] *= sizescale;
x[i][1] *= sizescale;
x[i][2] *= sizescale;
@@ -669,12 +680,8 @@ void Molecule::types(char *line)
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 2)
- error->all(FLERR,"Invalid Types section in molecule file");
- }
- sscanf(line,"%d %d",&tmp,&type[i]);
+ if (2 != sscanf(line,"%d %d",&tmp,&type[i]))
+ error->all(FLERR,"Invalid Types section in molecule file");
type[i] += toffset;
}
@@ -695,12 +702,8 @@ void Molecule::charges(char *line)
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 2)
- error->all(FLERR,"Invalid Charges section in molecule file");
- }
- sscanf(line,"%d %lg",&tmp,&q[i]);
+ if (2 != sscanf(line,"%d %lg",&tmp,&q[i]))
+ error->all(FLERR,"Invalid Charges section in molecule file");
}
}
@@ -714,12 +717,8 @@ void Molecule::diameters(char *line)
maxradius = 0.0;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 2)
- error->all(FLERR,"Invalid Diameters section in molecule file");
- }
- sscanf(line,"%d %lg",&tmp,&radius[i]);
+ if (2 != sscanf(line,"%d %lg",&tmp,&radius[i]))
+ error->all(FLERR,"Invalid Diameters section in molecule file");
radius[i] *= sizescale;
radius[i] *= 0.5;
maxradius = MAX(maxradius,radius[i]);
@@ -739,12 +738,8 @@ void Molecule::masses(char *line)
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 2)
- error->all(FLERR,"Invalid Masses section in molecule file");
- }
- sscanf(line,"%d %lg",&tmp,&rmass[i]);
+ if (2 != sscanf(line,"%d %lg",&tmp,&rmass[i]))
+ error->all(FLERR,"Invalid Masses section in molecule file");
rmass[i] *= sizescale*sizescale*sizescale;
}
@@ -773,17 +768,13 @@ void Molecule::bonds(int flag, char *line)
for (int i = 0; i < nbonds; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 4)
- error->all(FLERR,"Invalid Bonds section in molecule file");
- }
- sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&itype,&atom1,&atom2);
+ if (4 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&itype,&atom1,&atom2))
+ error->all(FLERR,"Invalid Bonds section in molecule file");
itype += boffset;
if (atom1 <= 0 || atom1 > natoms ||
- atom2 <= 0 || atom2 > natoms)
+ atom2 <= 0 || atom2 > natoms)
error->one(FLERR,"Invalid atom ID in Bonds section of molecule file");
if (itype <= 0)
error->one(FLERR,"Invalid bond type in Bonds section of molecule file");
@@ -795,10 +786,10 @@ void Molecule::bonds(int flag, char *line)
bond_atom[m][num_bond[m]] = atom2;
num_bond[m]++;
if (newton_bond == 0) {
- m = atom2-1;
- bond_type[m][num_bond[m]] = itype;
- bond_atom[m][num_bond[m]] = atom1;
- num_bond[m]++;
+ m = atom2-1;
+ bond_type[m][num_bond[m]] = itype;
+ bond_atom[m][num_bond[m]] = atom1;
+ num_bond[m]++;
}
} else {
count[atom1-1]++;
@@ -835,13 +826,9 @@ void Molecule::angles(int flag, char *line)
for (int i = 0; i < nangles; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 5)
- error->all(FLERR,"Invalid Angles section in molecule file");
- }
- sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&itype,&atom1,&atom2,&atom3);
+ if (5 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&itype,&atom1,&atom2,&atom3))
+ error->all(FLERR,"Invalid Angles section in molecule file");
itype += aoffset;
if (atom1 <= 0 || atom1 > natoms ||
@@ -860,24 +847,24 @@ void Molecule::angles(int flag, char *line)
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
if (newton_bond == 0) {
- m = atom1-1;
- angle_type[m][num_angle[m]] = itype;
- angle_atom1[m][num_angle[m]] = atom1;
- angle_atom2[m][num_angle[m]] = atom2;
- angle_atom3[m][num_angle[m]] = atom3;
- num_angle[m]++;
- m = atom3-1;
- angle_type[m][num_angle[m]] = itype;
- angle_atom1[m][num_angle[m]] = atom1;
- angle_atom2[m][num_angle[m]] = atom2;
- angle_atom3[m][num_angle[m]] = atom3;
- num_angle[m]++;
+ m = atom1-1;
+ angle_type[m][num_angle[m]] = itype;
+ angle_atom1[m][num_angle[m]] = atom1;
+ angle_atom2[m][num_angle[m]] = atom2;
+ angle_atom3[m][num_angle[m]] = atom3;
+ num_angle[m]++;
+ m = atom3-1;
+ angle_type[m][num_angle[m]] = itype;
+ angle_atom1[m][num_angle[m]] = atom1;
+ angle_atom2[m][num_angle[m]] = atom2;
+ angle_atom3[m][num_angle[m]] = atom3;
+ num_angle[m]++;
}
} else {
count[atom2-1]++;
if (newton_bond == 0) {
- count[atom1-1]++;
- count[atom3-1]++;
+ count[atom1-1]++;
+ count[atom3-1]++;
}
}
}
@@ -911,14 +898,10 @@ void Molecule::dihedrals(int flag, char *line)
for (int i = 0; i < ndihedrals; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 6)
- error->all(FLERR,"Invalid Dihedrals section in molecule file");
- }
- sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ if (6 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
- &tmp,&itype,&atom1,&atom2,&atom3,&atom4);
+ &tmp,&itype,&atom1,&atom2,&atom3,&atom4))
+ error->all(FLERR,"Invalid Dihedrals section in molecule file");
itype += doffset;
if (atom1 <= 0 || atom1 > natoms ||
@@ -926,10 +909,10 @@ void Molecule::dihedrals(int flag, char *line)
atom3 <= 0 || atom3 > natoms ||
atom4 <= 0 || atom4 > natoms)
error->one(FLERR,
- "Invalid atom ID in dihedrals section of molecule file");
+ "Invalid atom ID in dihedrals section of molecule file");
if (itype <= 0)
error->one(FLERR,
- "Invalid dihedral type in dihedrals section of molecule file");
+ "Invalid dihedral type in dihedrals section of molecule file");
if (flag) {
m = atom2-1;
@@ -941,34 +924,34 @@ void Molecule::dihedrals(int flag, char *line)
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
if (newton_bond == 0) {
- m = atom1-1;
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
- m = atom3-1;
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
- m = atom4-1;
- dihedral_type[m][num_dihedral[m]] = itype;
- dihedral_atom1[m][num_dihedral[m]] = atom1;
- dihedral_atom2[m][num_dihedral[m]] = atom2;
- dihedral_atom3[m][num_dihedral[m]] = atom3;
- dihedral_atom4[m][num_dihedral[m]] = atom4;
- num_dihedral[m]++;
+ m = atom1-1;
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
+ m = atom3-1;
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
+ m = atom4-1;
+ dihedral_type[m][num_dihedral[m]] = itype;
+ dihedral_atom1[m][num_dihedral[m]] = atom1;
+ dihedral_atom2[m][num_dihedral[m]] = atom2;
+ dihedral_atom3[m][num_dihedral[m]] = atom3;
+ dihedral_atom4[m][num_dihedral[m]] = atom4;
+ num_dihedral[m]++;
}
} else {
count[atom2-1]++;
if (newton_bond == 0) {
- count[atom1-1]++;
- count[atom3-1]++;
- count[atom4-1]++;
+ count[atom1-1]++;
+ count[atom3-1]++;
+ count[atom4-1]++;
}
}
}
@@ -1002,14 +985,10 @@ void Molecule::impropers(int flag, char *line)
for (int i = 0; i < nimpropers; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 6)
- error->all(FLERR,"Invalid Impropers section in molecule file");
- }
- sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ if (6 != sscanf(line,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " "
TAGINT_FORMAT " " TAGINT_FORMAT " ",
- &tmp,&itype,&atom1,&atom2,&atom3,&atom4);
+ &tmp,&itype,&atom1,&atom2,&atom3,&atom4))
+ error->all(FLERR,"Invalid Impropers section in molecule file");
itype += ioffset;
if (atom1 <= 0 || atom1 > natoms ||
@@ -1017,10 +996,10 @@ void Molecule::impropers(int flag, char *line)
atom3 <= 0 || atom3 > natoms ||
atom4 <= 0 || atom4 > natoms)
error->one(FLERR,
- "Invalid atom ID in impropers section of molecule file");
+ "Invalid atom ID in impropers section of molecule file");
if (itype <= 0)
error->one(FLERR,
- "Invalid improper type in impropers section of molecule file");
+ "Invalid improper type in impropers section of molecule file");
if (flag) {
m = atom2-1;
@@ -1032,34 +1011,34 @@ void Molecule::impropers(int flag, char *line)
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
if (newton_bond == 0) {
- m = atom1-1;
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
- m = atom3-1;
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
- m = atom4-1;
- improper_type[m][num_improper[m]] = itype;
- improper_atom1[m][num_improper[m]] = atom1;
- improper_atom2[m][num_improper[m]] = atom2;
- improper_atom3[m][num_improper[m]] = atom3;
- improper_atom4[m][num_improper[m]] = atom4;
- num_improper[m]++;
+ m = atom1-1;
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
+ m = atom3-1;
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
+ m = atom4-1;
+ improper_type[m][num_improper[m]] = itype;
+ improper_atom1[m][num_improper[m]] = atom1;
+ improper_atom2[m][num_improper[m]] = atom2;
+ improper_atom3[m][num_improper[m]] = atom3;
+ improper_atom4[m][num_improper[m]] = atom4;
+ num_improper[m]++;
}
} else {
count[atom2-1]++;
if (newton_bond == 0) {
- count[atom1-1]++;
- count[atom3-1]++;
- count[atom4-1]++;
+ count[atom1-1]++;
+ count[atom3-1]++;
+ count[atom4-1]++;
}
}
}
@@ -1087,13 +1066,9 @@ void Molecule::nspecial_read(int flag, char *line)
for (int i = 0; i < natoms; i++) {
readline(line);
- if (i == 0) {
- int nwords = atom->count_words(line);
- if (nwords != 4)
- error->all(FLERR,"Invalid Special Bond Counts section in "
- "molecule file");
- }
- sscanf(line,"%d %d %d %d",&tmp,&c1,&c2,&c3);
+ if (4 != sscanf(line,"%d %d %d %d",&tmp,&c1,&c2,&c3))
+ error->all(FLERR,"Invalid Special Bond Counts section in "
+ "molecule file");
if (flag) {
nspecial[i][0] = c1;
@@ -1117,13 +1092,13 @@ void Molecule::special_read(char *line)
nwords = parse(line,words,maxspecial+1);
if (nwords != nspecial[i][2]+1)
error->all(FLERR,"Molecule file special list "
- "does not match special count");
+ "does not match special count");
for (m = 1; m < nwords; m++) {
special[i][m-1] = ATOTAGINT(words[m]);
if (special[i][m-1] <= 0 || special[i][m-1] > natoms ||
- special[i][m-1] == i+1)
- error->all(FLERR,"Invalid special atom index in molecule file");
+ special[i][m-1] == i+1)
+ error->all(FLERR,"Invalid special atom index in molecule file");
}
}
@@ -1229,7 +1204,8 @@ void Molecule::shakeflag_read(char *line)
int tmp;
for (int i = 0; i < natoms; i++) {
readline(line);
- sscanf(line,"%d %d",&tmp,&shake_flag[i]);
+ if (2 != sscanf(line,"%d %d",&tmp,&shake_flag[i]))
+ error->all(FLERR,"Invalid Shake Flags section in molecule file");
}
for (int i = 0; i < natoms; i++)
@@ -1243,23 +1219,32 @@ void Molecule::shakeflag_read(char *line)
void Molecule::shakeatom_read(char *line)
{
- int tmp;
+ int tmp, nmatch, nwant;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (shake_flag[i] == 1)
- sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
- else if (shake_flag[i] == 2)
- sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&shake_atom[i][0],&shake_atom[i][1]);
- else if (shake_flag[i] == 3)
- sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&shake_atom[i][0],&shake_atom[i][1],&shake_atom[i][2]);
- else if (shake_flag[i] == 4)
- sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
- TAGINT_FORMAT " " TAGINT_FORMAT,
- &tmp,&shake_atom[i][0],&shake_atom[i][1],
- &shake_atom[i][2],&shake_atom[i][3]);
+ if (shake_flag[i] == 1) {
+ nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT
+ " " TAGINT_FORMAT,&tmp,&shake_atom[i][0],
+ &shake_atom[i][1],&shake_atom[i][2]);
+ nwant = 4;
+ } else if (shake_flag[i] == 2) {
+ nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&shake_atom[i][0],&shake_atom[i][1]);
+ nwant = 3;
+ } else if (shake_flag[i] == 3) {
+ nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT
+ " " TAGINT_FORMAT,&tmp,&shake_atom[i][0],
+ &shake_atom[i][1],&shake_atom[i][2]);
+ nwant = 4;
+ } else if (shake_flag[i] == 4) {
+ nmatch = sscanf(line,"%d " TAGINT_FORMAT " " TAGINT_FORMAT " "
+ TAGINT_FORMAT " " TAGINT_FORMAT,
+ &tmp,&shake_atom[i][0],&shake_atom[i][1],
+ &shake_atom[i][2],&shake_atom[i][3]);
+ nwant = 5;
+ }
+ if (nmatch != nwant)
+ error->all(FLERR,"Invalid shake atom in molecule file");
}
for (int i = 0; i < natoms; i++) {
@@ -1277,19 +1262,27 @@ void Molecule::shakeatom_read(char *line)
void Molecule::shaketype_read(char *line)
{
- int tmp;
+ int tmp,nmatch,nwant;
for (int i = 0; i < natoms; i++) {
readline(line);
- if (shake_flag[i] == 1)
- sscanf(line,"%d %d %d %d",&tmp,
- &shake_type[i][0],&shake_type[i][1],&shake_type[i][2]);
- else if (shake_flag[i] == 2)
- sscanf(line,"%d %d",&tmp,&shake_type[i][0]);
- else if (shake_flag[i] == 3)
- sscanf(line,"%d %d %d",&tmp,&shake_type[i][0],&shake_type[i][1]);
- else if (shake_flag[i] == 4)
- sscanf(line,"%d %d %d %d",&tmp,
- &shake_type[i][0],&shake_type[i][1],&shake_type[i][2]);
+ if (shake_flag[i] == 1) {
+ nmatch = sscanf(line,"%d %d %d %d",&tmp,&shake_type[i][0],
+ &shake_type[i][1],&shake_type[i][2]);
+ nwant = 4;
+ } else if (shake_flag[i] == 2) {
+ nmatch = sscanf(line,"%d %d",&tmp,&shake_type[i][0]);
+ nwant = 2;
+ } else if (shake_flag[i] == 3) {
+ nmatch = sscanf(line,"%d %d %d",&tmp,&shake_type[i][0],
+ &shake_type[i][1]);
+ nwant = 3;
+ } else if (shake_flag[i] == 4) {
+ nmatch = sscanf(line,"%d %d %d %d",&tmp,&shake_type[i][0],
+ &shake_type[i][1],&shake_type[i][2]);
+ nwant = 4;
+ }
+ if (nmatch != nwant)
+ error->all(FLERR,"Invalid shake type data in molecule file");
}
for (int i = 0; i < natoms; i++) {
@@ -1501,46 +1494,46 @@ void Molecule::allocate()
if (bondflag) {
memory->create(bond_type,natoms,bond_per_atom,
- "molecule:bond_type");
+ "molecule:bond_type");
memory->create(bond_atom,natoms,bond_per_atom,
- "molecule:bond_atom");
+ "molecule:bond_atom");
}
if (angleflag) {
memory->create(angle_type,natoms,angle_per_atom,
- "molecule:angle_type");
+ "molecule:angle_type");
memory->create(angle_atom1,natoms,angle_per_atom,
- "molecule:angle_atom1");
+ "molecule:angle_atom1");
memory->create(angle_atom2,natoms,angle_per_atom,
- "molecule:angle_atom2");
+ "molecule:angle_atom2");
memory->create(angle_atom3,natoms,angle_per_atom,
- "molecule:angle_atom3");
+ "molecule:angle_atom3");
}
if (dihedralflag) {
memory->create(dihedral_type,natoms,dihedral_per_atom,
- "molecule:dihedral_type");
+ "molecule:dihedral_type");
memory->create(dihedral_atom1,natoms,dihedral_per_atom,
- "molecule:dihedral_atom1");
+ "molecule:dihedral_atom1");
memory->create(dihedral_atom2,natoms,dihedral_per_atom,
- "molecule:dihedral_atom2");
+ "molecule:dihedral_atom2");
memory->create(dihedral_atom3,natoms,dihedral_per_atom,
- "molecule:dihedral_atom3");
+ "molecule:dihedral_atom3");
memory->create(dihedral_atom4,natoms,dihedral_per_atom,
- "molecule:dihedral_atom4");
+ "molecule:dihedral_atom4");
}
if (improperflag) {
memory->create(improper_type,natoms,improper_per_atom,
- "molecule:improper_type");
+ "molecule:improper_type");
memory->create(improper_atom1,natoms,improper_per_atom,
- "molecule:improper_atom1");
+ "molecule:improper_atom1");
memory->create(improper_atom2,natoms,improper_per_atom,
- "molecule:improper_atom2");
+ "molecule:improper_atom2");
memory->create(improper_atom3,natoms,improper_per_atom,
- "molecule:improper_atom3");
+ "molecule:improper_atom3");
memory->create(improper_atom4,natoms,improper_per_atom,
- "molecule:improper_atom4");
+ "molecule:improper_atom4");
}
if (shakeflag) {
@@ -1653,7 +1646,7 @@ void Molecule::parse_keyword(int flag, char *line, char *keyword)
if (me == 0) {
if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
while (eof == 0 && strspn(line," \t\n\r") == strlen(line)) {
- if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
+ if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
}
if (fgets(keyword,MAXLINE,fp) == NULL) eof = 1;
}
diff --git a/tools/msi2lmp/README b/tools/msi2lmp/README
index db9b1aca5efeec6f0d68dcf6539351426046f0d9..9ac7af560743a7f71853dd619ad012c778de0ef5 100644
--- a/tools/msi2lmp/README
+++ b/tools/msi2lmp/README
@@ -140,6 +140,8 @@ msi2lmp has the following known limitations:
- there is no support for auto-equivalences to supplement fully
parameterized interactions with heuristic ones
- there is no support for bond increments
+- there is no support for coordinates defined by symmetry operations,
+ i.e. the .mdf file has to be set up for space group P1
------------------------------------------------------------------------