Collected small changes and fixes

doc/src/pair_ilp_tmd.rst

@@ -22,12 +22,12 @@ Examples
 .. code-block:: LAMMPS
 
    pair_style  hybrid/overlay ilp/tmd 16.0 1
-   pair_coeff  * * ilp/tmd  TMD.ILP Mo S S
+   pair_coeff  * * ilp/tmd  MoS2.ILP Mo S S
 
    pair_style  hybrid/overlay sw/mod sw/mod ilp/tmd 16.0
    pair_coeff  * * sw/mod 1  tmd.sw.mod Mo S S NULL NULL NULL
    pair_coeff  * * sw/mod 2  tmd.sw.mod NULL NULL NULL Mo S S
-   pair_coeff  * * ilp/tmd   TMD.ILP    Mo S S Mo S S
+   pair_coeff  * * ilp/tmd   MoS2.ILP   Mo S S Mo S S
 
 Description
 """""""""""
@@ -69,15 +69,15 @@ calculating the normals.
    each atom `i`, its six nearest neighboring atoms belonging to the same
    sub-layer are chosen to define the normal vector `{\bf n}_i`.
 
-The parameter file (e.g. TMD.ILP), is intended for use with *metal*
+The parameter file (e.g. MoS2.ILP), is intended for use with *metal*
 :doc:`units <units>`, with energies in meV. Two additional parameters,
 *S*, and *rcut* are included in the parameter file. *S* is designed to
 facilitate scaling of energies. *rcut* is designed to build the neighbor
 list for calculating the normals for each atom pair.
 
 .. note::
 
-   The parameters presented in the parameter file (e.g. TMD.ILP),
+   The parameters presented in the parameter file (e.g. MoS2.ILP),
    are fitted with taper function by setting the cutoff equal to 16.0
    Angstrom.  Using different cutoff or taper function should be careful.
    These parameters provide a good description in both short- and long-range
@@ -133,10 +133,10 @@ if LAMMPS was built with that package.  See the :doc:`Build package
 This pair style requires the newton setting to be *on* for pair
 interactions.
 
-The TMD.ILP potential file provided with LAMMPS (see the potentials
+The MoS2.ILP potential file provided with LAMMPS (see the potentials
 directory) are parameterized for *metal* units.  You can use this
 potential with any LAMMPS units, but you would need to create your own
-custom TMD.ILP potential file with coefficients listed in the appropriate
+custom MoS2.ILP potential file with coefficients listed in the appropriate
 units, if your simulation does not use *metal* units.
 
 Related commands

doc/src/pair_reaxff.rst

@@ -43,22 +43,22 @@ Examples
 Description
 """""""""""
 
-Style *reaxff* computes the ReaxFF potential of van Duin, Goddard and
-co-workers.  ReaxFF uses distance-dependent bond-order functions to
+Pair style *reaxff* computes the ReaxFF potential of van Duin, Goddard
+and co-workers.  ReaxFF uses distance-dependent bond-order functions to
 represent the contributions of chemical bonding to the potential
-energy. There is more than one version of ReaxFF. The version
+energy.  There is more than one version of ReaxFF.  The version
 implemented in LAMMPS uses the functional forms documented in the
 supplemental information of the following paper:
-:ref:`(Chenoweth et al., 2008) <Chenoweth_20082>`.  The version integrated
-into LAMMPS matches the version of ReaxFF From Summer 2010.  For more
-technical details about the pair reaxff implementation of ReaxFF, see
-the :ref:`(Aktulga) <Aktulga>` paper. The *reaxff* style was initially
-implemented as a stand-alone C code and is now converted to C++ and
-integrated into LAMMPS as a package.
+:ref:`(Chenoweth et al., 2008) <Chenoweth_20082>` and matches the
+version of the reference ReaxFF implementation from Summer 2010.  For
+more technical details about the implementation of ReaxFF in pair style
+*reaxff*, see the :ref:`(Aktulga) <Aktulga>` paper. The *reaxff* style
+was initially implemented as a stand-alone C code and is now converted
+to C++ and integrated into LAMMPS as a package.
 
 The *reaxff/kk* style is a Kokkos version of the ReaxFF potential that
-is derived from the *reaxff* style. The Kokkos version can run on GPUs
-and can also use OpenMP multithreading. For more information about the
+is derived from the *reaxff* style.  The Kokkos version can run on GPUs
+and can also use OpenMP multithreading.  For more information about the
 Kokkos package, see :doc:`Packages details <Packages_details>` and
 :doc:`Speed kokkos <Speed_kokkos>` doc pages.  One important
 consideration when using the *reaxff/kk* style is the choice of either

lib/pace/Makefile

@@ -1,4 +1,5 @@
 SHELL = /bin/sh
+CMAKE= cmake
 
 # ------ FILES ------
 
@@ -35,7 +36,7 @@ lib: $(OBJ) lib-yaml-cpp
 
 
 lib-yaml-cpp:
-	cd $(YAML_CPP_PATH) && $(MAKE) lib
+	cd $(YAML_CPP_PATH) && $(CMAKE) . && $(MAKE) all
 
 # ------ COMPILE RULES ------
 
@@ -45,9 +46,8 @@ lib-yaml-cpp:
 # ------ CLEAN ------
 clean-all:
 	-rm -f *~ $(OBJ) $(LIB)
-	cd $(YAML_CPP_PATH) && $(MAKE) clean-all
+	cd $(YAML_CPP_PATH) && $(MAKE) clean
 
 clean-build:
 	-rm -f *~ $(OBJ)
-	cd $(YAML_CPP_PATH) && $(MAKE) clean-build
 

lib/pace/Makefile.lammps

@@ -1,3 +1,3 @@
 pace_SYSINC =-I../../lib/pace/src/ML-PACE -I../../lib/pace/src/yaml-cpp/include -I../../lib/pace/src/wigner-cpp/include -DEXTRA_C_PROJECTIONS
-pace_SYSLIB = -L../../lib/pace/ -lpace -L../../lib/pace/src/yaml-cpp/ -lyaml-cpp
+pace_SYSLIB = -L../../lib/pace/ -lpace -L../../lib/pace/src/yaml-cpp/ -lyaml-cpp-pace
 pace_SYSPATH =

src/OPENMP/npair_omp.h

@@ -32,6 +32,7 @@ namespace LAMMPS_NS {
 // get access to number of threads and per-thread data structures via FixOMP
 #define NPAIR_OMP_INIT                 \
   const int nthreads = comm->nthreads; \
+  omp_set_num_threads(nthreads); \
   const int ifix = modify->find_fix("package_omp")
 
 // get thread id and then assign each thread a fixed chunk of atoms

src/compute_msd_chunk.cpp

@@ -27,8 +27,8 @@ using namespace LAMMPS_NS;
 /* ---------------------------------------------------------------------- */
 
 ComputeMSDChunk::ComputeMSDChunk(LAMMPS *lmp, int narg, char **arg) :
-    ComputeChunk(lmp, narg, arg), id_fix(nullptr), massproc(nullptr), masstotal(nullptr),
-    com(nullptr), comall(nullptr), msd(nullptr)
+    ComputeChunk(lmp, narg, arg), id_fix(nullptr), fix(nullptr), massproc(nullptr),
+    masstotal(nullptr), com(nullptr), comall(nullptr), msd(nullptr)
 {
   if (narg != 4) error->all(FLERR, "Illegal compute msd/chunk command");
 
@@ -196,6 +196,12 @@ void ComputeMSDChunk::compute_array()
 void ComputeMSDChunk::allocate()
 {
   ComputeChunk::allocate();
+  memory->destroy(massproc);
+  memory->destroy(masstotal);
+  memory->destroy(com);
+  memory->destroy(comall);
+  memory->destroy(msd);
+
   memory->create(massproc, nchunk, "msd/chunk:massproc");
   memory->create(masstotal, nchunk, "msd/chunk:masstotal");
   memory->create(com, nchunk, 3, "msd/chunk:com");

tools/lammps-gui/codeeditor.cpp

@@ -564,7 +564,7 @@ void CodeEditor::keyPressEvent(QKeyEvent *event)
     // process key event in parent class
     QPlainTextEdit::keyPressEvent(event);
 
-    // if enabled, try pop up completion automatically after 3 characters
+    // if enabled, try pop up completion automatically after 2 characters
     if (automatic_completion) {
         auto cursor = textCursor();
         auto line   = cursor.block().text();
@@ -990,8 +990,26 @@ void CodeEditor::insertCompletedCommand(const QString &completion)
 {
     auto *completer = qobject_cast<QCompleter *>(sender());
     if (completer->widget() != this) return;
+
+    // select the entire word (non-space text) under the cursor
+    // we need to do it in this compicated way, since QTextCursor does not recognize
+    // special characters as part of a word.
     auto cursor = textCursor();
-    cursor.movePosition(QTextCursor::StartOfWord, QTextCursor::KeepAnchor);
+    auto line   = cursor.block().text();
+    int begin   = cursor.positionInBlock();
+    do {
+        if (line[begin].isSpace()) break;
+        --begin;
+    } while (begin >= 0);
+
+    int end = begin + 1;
+    while (end < line.length()) {
+        if (line[end].isSpace()) break;
+        ++end;
+    }
+
+    cursor.setPosition(cursor.position() - cursor.positionInBlock() + begin + 1);
+    cursor.movePosition(QTextCursor::NextCharacter, QTextCursor::KeepAnchor, end - begin - 1);
     cursor.insertText(completion);
     setTextCursor(cursor);
 }

tools/lammps-gui/imageviewer.cpp

@@ -131,7 +131,7 @@ static const QString blank(" ");
 
 ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidget *parent) :
     QDialog(parent), menuBar(new QMenuBar), imageLabel(new QLabel), scrollArea(new QScrollArea),
-    lammps(_lammps), group("all"), filename(fileName), useelements(false)
+    lammps(_lammps), group("all"), filename(fileName), useelements(false), usediameter(false)
 {
     imageLabel->setBackgroundRole(QPalette::Base);
     imageLabel->setSizePolicy(QSizePolicy::Ignored, QSizePolicy::Ignored);
@@ -268,7 +268,7 @@ ImageViewer::ImageViewer(const QString &fileName, LammpsWrapper *_lammps, QWidge
     // properties directly since lookup in reset_view() will have failed
     dobox->setChecked(showbox);
     dovdw->setChecked(vdwfactor > 1.0);
-    dovdw->setEnabled(useelements);
+    dovdw->setEnabled(useelements || usediameter);
     doaxes->setChecked(showaxes);
     dossao->setChecked(usessao);
     doanti->setChecked(antialias);
@@ -435,7 +435,7 @@ void ImageViewer::createImage()
     dumpcmd += "'" + dumpfile.fileName() + "'";
 
     settings.beginGroup("snapshot");
-    int hhrot    = (hrot > 180) ? 360 - hrot : hrot;
+    int hhrot = (hrot > 180) ? 360 - hrot : hrot;
 
     // determine elements from masses and set their covalent radii
     int ntypes       = lammps->extract_setting("ntypes");
@@ -454,9 +454,10 @@ void ImageViewer::createImage()
             adiams += QString("adiam %1 %2 ").arg(i).arg(vdwfactor * pte_vdw_radius[idx]);
         }
     }
+    usediameter = lammps->extract_setting("radius_flag") != 0;
 
     // adjust pushbutton state and clear adiams string to disable VDW display, if needed
-    if (useelements) {
+    if (useelements || usediameter) {
         auto *button = findChild<QPushButton *>("vdw");
         if (button) button->setEnabled(true);
     } else {
@@ -469,7 +470,10 @@ void ImageViewer::createImage()
         dumpcmd += blank + "element";
     else
         dumpcmd += blank + settings.value("color", "type").toString();
-    dumpcmd += blank + settings.value("diameter", "type").toString();
+    if (usediameter && (vdwfactor > 1.0))
+        dumpcmd += blank + "diameter";
+    else
+        dumpcmd += blank + settings.value("diameter", "type").toString();
     dumpcmd += QString(" size %1 %2").arg(xsize).arg(ysize);
     dumpcmd += QString(" zoom %1").arg(zoom);
     dumpcmd += " shiny 0.5 ";

tools/lammps-gui/imageviewer.h

@@ -88,7 +88,7 @@ private slots:
     int xsize, ysize;
     int hrot, vrot;
     double zoom, vdwfactor;
-    bool showbox, showaxes, antialias, usessao, useelements;
+    bool showbox, showaxes, antialias, usessao, useelements, usediameter;
 };
 #endif
 

tools/lammps-gui/stdcapture.cpp

@@ -77,6 +77,7 @@ bool StdCapture::EndCapture()
 
     int bytesRead;
     bool fd_blocked;
+    int maxwait = 100;
 
     do {
         bytesRead  = 0;
@@ -93,9 +94,10 @@ bool StdCapture::EndCapture()
             buf[bytesRead] = 0;
             m_captured += buf;
         } else if (bytesRead < 0) {
-            fd_blocked = ((errno == EAGAIN) || (errno == EWOULDBLOCK) || (errno == EINTR));
+            fd_blocked = ((errno == EAGAIN) || (errno == EWOULDBLOCK) || (errno == EINTR)) && (maxwait > 0);
 
             if (fd_blocked) std::this_thread::sleep_for(std::chrono::milliseconds(10));
+            --maxwait;
         }
     } while (fd_blocked || (bytesRead == (bufSize - 1)));
     m_capturing = false;