From 5dc09ae3c0ad3c8e790f26b232b04b255ea14bb7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 27 Oct 2020 15:04:05 -0400 Subject: [PATCH 1/7] increase timeout, properly handle timeouts, and fix symbol lookup in exception handling --- unittest/tools/test_lammps_shell.py | 109 ++++++++++++++++++---------- 1 file changed, 72 insertions(+), 37 deletions(-) diff --git a/unittest/tools/test_lammps_shell.py b/unittest/tools/test_lammps_shell.py index afbbca033b..1768bcf753 100644 --- a/unittest/tools/test_lammps_shell.py +++ b/unittest/tools/test_lammps_shell.py @@ -22,68 +22,97 @@ class LammpsShell(unittest.TestCase): def InputRunner(self,text): """Test tab expansions""" try: - [outs,errs] = self.proc.communicate(input=text, timeout=1) - except TimeoutExpired: - proc.kill() - [outs,errs] = proc.communicate() + [outs,errs] = self.proc.communicate(input=text, timeout=10) + self.timeout = 0 + except subprocess.TimeoutExpired: + self.proc.kill() + [outs,errs] = self.proc.communicate() + self.timeout = 1 return outs.decode('UTF-8') def testExpandClearHistory(self): """Test expansion of a shell specific command""" matches = re.findall(shell_prompt_re, self.InputRunner(b'clear_his\t\n'), re.MULTILINE) - self.assertEqual(matches[0][1],"clear_history") + if self.timeout: + self.fail("Timeout") + else: + self.assertEqual(matches[0][1],"clear_history") def testExpandDimension(self): """Test expansion of a LAMMPS command""" matches = re.findall(shell_prompt_re, self.InputRunner(b'dimens\t\n'), re.MULTILINE) - self.assertEqual(matches[0][1],"dimension") + if self.timeout: + self.fail("Timeout") + else: + self.assertEqual(matches[0][1],"dimension") def testExpandPairStyle(self): """Test expansion of a pair style""" matches = re.findall(shell_prompt_re, self.InputRunner(b'pair_st\t zer\t\n'), re.MULTILINE) - self.assertEqual(matches[0][1],"pair_style") - self.assertEqual(matches[0][2],"zero") + if self.timeout: + self.fail("Timeout") + else: + self.assertEqual(matches[0][1],"pair_style") + self.assertEqual(matches[0][2],"zero") def testExpandBondStyle(self): """Test expansion of a bond style""" matches = re.findall(shell_prompt_re, self.InputRunner(b'bond_st\t zer\t\n'), re.MULTILINE) - self.assertEqual(matches[0][1],"bond_style") - self.assertEqual(matches[0][2],"zero") + if self.timeout: + self.fail("Timeout") + else: + self.assertEqual(matches[0][1],"bond_style") + self.assertEqual(matches[0][2],"zero") def testExpandAngleStyle(self): """Test expansion of a angle style""" matches = re.findall(shell_prompt_re, self.InputRunner(b'angle_st\t zer\t\n'), re.MULTILINE) - self.assertEqual(matches[0][1],"angle_style") - self.assertEqual(matches[0][2],"zero") + if self.timeout: + self.fail("Timeout") + else: + self.assertEqual(matches[0][1],"angle_style") + self.assertEqual(matches[0][2],"zero") def testExpandDihedralStyle(self): """Test expansion of a dihedral style""" matches = re.findall(shell_prompt_re, self.InputRunner(b'dihedral_st\t zer\t\n'), re.MULTILINE) - self.assertEqual(matches[0][1],"dihedral_style") - self.assertEqual(matches[0][2],"zero") + if self.timeout: + self.fail("Timeout") + else: + self.assertEqual(matches[0][1],"dihedral_style") + self.assertEqual(matches[0][2],"zero") def testExpandImproperStyle(self): """Test expansion of a improper style""" matches = re.findall(shell_prompt_re, self.InputRunner(b'improper_st\t zer\t\n'), re.MULTILINE) - self.assertEqual(matches[0][1],"improper_style") - self.assertEqual(matches[0][2],"zero") + if self.timeout: + self.fail("Timeout") + else: + self.assertEqual(matches[0][1],"improper_style") + self.assertEqual(matches[0][2],"zero") def testExpandComputeGroup(self): """Test expansion of a group-ID and a compute command""" matches = re.findall(cmd_group_re, self.InputRunner(b'compute test al\tcentro/at\t\n'), re.MULTILINE) - self.assertEqual(matches[0][1],"compute") - self.assertEqual(matches[0][2],"test") - self.assertEqual(matches[0][3],"all") - self.assertEqual(matches[0][4],"centro/atom") + if self.timeout: + self.fail("Timeout") + else: + self.assertEqual(matches[0][1],"compute") + self.assertEqual(matches[0][2],"test") + self.assertEqual(matches[0][3],"all") + self.assertEqual(matches[0][4],"centro/atom") def testExpandFixGroup(self): """Test expansion of a group-ID and a fix command""" matches = re.findall(cmd_group_re, self.InputRunner(b'fix test al\tcontroll\t\n'), re.MULTILINE) - self.assertEqual(matches[0][1],"fix") - self.assertEqual(matches[0][2],"test") - self.assertEqual(matches[0][3],"all") - self.assertEqual(matches[0][4],"controller") + if self.timeout: + self.fail("Timeout") + else: + self.assertEqual(matches[0][1],"fix") + self.assertEqual(matches[0][2],"test") + self.assertEqual(matches[0][3],"all") + self.assertEqual(matches[0][4],"controller") def testExpandSource(self): """Test expansion of a shell command and a file name""" @@ -92,24 +121,30 @@ class LammpsShell(unittest.TestCase): out.close() matches = re.findall(shell_prompt_re, self.InputRunner(b'sour\t.tmp.in.sou\t\n'), re.MULTILINE) os.remove('.tmp.in.source') - self.assertEqual(matches[0][1],"source") - self.assertEqual(matches[0][2],".tmp.in.source") + if self.timeout: + self.fail("Timeout") + else: + self.assertEqual(matches[0][1],"source") + self.assertEqual(matches[0][2],".tmp.in.source") def testHistory(self): """Test history expansion""" out = self.InputRunner(b'clear_history\nunits real\ndimension 2\n!!:p\n!-3:p\n!dim:p\n!uni:p\nprint !!:$\nprint !dim:1\n') idx = 0 - lines = out.splitlines() - for line in lines: - if line.startswith('LAMMPS Shell>'): break - idx += 1 - - self.assertEqual(lines[idx+4],"dimension 2") - self.assertEqual(lines[idx+6],"units real") - self.assertEqual(lines[idx+8],"dimension 2") - self.assertEqual(lines[idx+10],"units real") - self.assertEqual(lines[idx+12],"real") - self.assertEqual(lines[idx+14],"2") + if self.timeout: + self.fail("Timeout") + else: + lines = out.splitlines() + for line in lines: + if line.startswith('LAMMPS Shell>'): break + idx += 1 + + self.assertEqual(lines[idx+4],"dimension 2") + self.assertEqual(lines[idx+6],"units real") + self.assertEqual(lines[idx+8],"dimension 2") + self.assertEqual(lines[idx+10],"units real") + self.assertEqual(lines[idx+12],"real") + self.assertEqual(lines[idx+14],"2") ########################### if __name__ == "__main__": From 9a3f935c9b213f719ee4c82d3f5eef1d9be9b9d4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 27 Oct 2020 17:50:57 -0400 Subject: [PATCH 2/7] do not include polyfill.js anymore --- cmake/Modules/Documentation.cmake | 10 ++-------- doc/Makefile | 12 ++---------- doc/src/Build_manual.rst | 4 ++-- .../sphinx-config/_themes/lammps_theme/layout.html | 5 ----- 4 files changed, 6 insertions(+), 25 deletions(-) diff --git a/cmake/Modules/Documentation.cmake b/cmake/Modules/Documentation.cmake index 6125155ad5..189c32e301 100644 --- a/cmake/Modules/Documentation.cmake +++ b/cmake/Modules/Documentation.cmake @@ -57,20 +57,14 @@ if(BUILD_DOC) # download mathjax distribution and unpack to folder "mathjax" if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5) - file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.0.5.tar.gz" + file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz" - EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7) + EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53) execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*) execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax) endif() - # for increased browser compatibility - if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/polyfill.js) - file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6" - "${DOC_BUILD_STATIC_DIR}/polyfill.js") - endif() - # set up doxygen and add targets to run it file(MAKE_DIRECTORY ${DOXYGEN_BUILD_DIR}) file(COPY ${LAMMPS_DOC_DIR}/doxygen/lammps-logo.png DESTINATION ${DOXYGEN_BUILD_DIR}/lammps-logo.png) diff --git a/doc/Makefile b/doc/Makefile index 18fba1bab4..59700f03aa 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -14,7 +14,6 @@ TXT2RST = $(VENV)/bin/txt2rst ANCHORCHECK = $(VENV)/bin/rst_anchor_check SPHINXCONFIG = $(BUILDDIR)/utils/sphinx-config MATHJAX = $(SPHINXCONFIG)/_static/mathjax -POLYFILL = $(SPHINXCONFIG)/_static/polyfill.js PYTHON = $(shell which python3) DOXYGEN = $(shell which doxygen) @@ -81,7 +80,7 @@ help: # ------------------------------------------ clean-all: clean - rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(POLYFILL) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf + rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf clean: clean-spelling rm -rf $(BUILDDIR)/html $(BUILDDIR)/epub $(BUILDDIR)/latex $(BUILDDIR)/doctrees $(BUILDDIR)/doxygen/xml $(BUILDDIR)/doxygen-warn.log $(BUILDDIR)/doxygen/Doxyfile $(SPHINXCONFIG)/conf.py @@ -95,7 +94,7 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in -e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \ -e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@ -html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) $(POLYFILL) +html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) @if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi @$(MAKE) $(MFLAGS) -C graphviz all @(\ @@ -237,13 +236,6 @@ $(VENV): $(MATHJAX): @git clone --depth 1 https://github.com/mathjax/MathJax.git $@ -# fall back to using wget and/or unencrypted download, if curl fails -$(POLYFILL): $(MATHJAX) - @curl -s -o $@ "https://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1 || \ - curl -s -o $@ "http://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1 || \ - wget -O $@ "https://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1 || \ - wget -O $@ "http://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1 - $(TXT2RST) $(ANCHORCHECK): $(VENV) @( \ . $(VENV)/bin/activate; \ diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst index 129e256cfd..59e4e3235b 100644 --- a/doc/src/Build_manual.rst +++ b/doc/src/Build_manual.rst @@ -73,8 +73,8 @@ after the documentation folder is returned to a pristine state with For the documentation build a python virtual environment is set up in the folder ``doc/docenv`` and various python packages are installed into that virtual environment via the ``pip`` tool. For rendering embedded -LaTeX code also the `MathJax `_ and the -`Polyfill `_ JavaScript engines need to be downloaded. +LaTeX code also the `MathJax `_ JavaScript +engine needs to be downloaded. The actual translation is then done via ``make`` commands in the doc folder. The following ``make`` commands are available: diff --git a/doc/utils/sphinx-config/_themes/lammps_theme/layout.html b/doc/utils/sphinx-config/_themes/lammps_theme/layout.html index 98d25ebca1..845f213a4c 100644 --- a/doc/utils/sphinx-config/_themes/lammps_theme/layout.html +++ b/doc/utils/sphinx-config/_themes/lammps_theme/layout.html @@ -52,11 +52,6 @@ {# Keep modernizr in head - http://modernizr.com/docs/#installing #} - {# for improved browser compatibility #} - - {%- if not embedded %} {# XXX Sphinx 1.8.0 made this an external js-file, quick fix until we refactor the template to inherert more blocks directly from sphinx #} {% if sphinx_version >= "1.8.0" %} From 94f57d88492b5c68e3800972e06fba00c45d4b16 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 28 Oct 2020 04:49:09 -0400 Subject: [PATCH 3/7] rephrase paragraph about availability of the manual and add note about browser compatibility --- doc/src/Manual.rst | 26 ++++++++++++++++++++++---- 1 file changed, 22 insertions(+), 4 deletions(-) diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index 88e2497c98..9198f545bc 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -21,10 +21,16 @@ where all LAMMPS development is coordinated. ---------- -The content for this manual is part of the LAMMPS distribution. You can -build a local copy of the Manual as HTML pages or a PDF file, by -following the steps on the :doc:`Build_manual` page. The manual is -organized in two parts: +The content for this manual is part of the LAMMPS distribution. The +online version always corresponds to the latest development version. +If needed, you can download or build a local copy of the manual as +HTML pages or a PDF file by following the steps on the +:doc:`Build_manual` page. If you have difficulties viewing the pages +please :ref:`see this note `. + +----------- + +The manual is organized in two parts: 1) the :ref:`User Guide ` for how to install and use LAMMPS and 2) the :ref:`Programmer Guide ` for how to write programs using the LAMMPS library from different @@ -107,3 +113,15 @@ Indices and tables * :ref:`genindex` * :ref:`search` + +.. _webbrowser: +.. admonition:: Web Browser Compatibility + + The HTML version of the manual makes use of advanced features present + int "modern" web browsers. This can lead to incompatibilities with older + web browsers (released more than 4 years ago) and specific vendor browsers + (e.g. Internet Explorer on Windows; Microsoft Edge works well though) + where parts of the pages are not rendered as expected (e.g. the layout is + broken or mathematical expressions not typeset). In that case we + recommend to install/use a different/newer web browser or use + the `PDF version of the manual `_. From 94462bfb487bc26dc0d6c11ab470c09252c5fc52 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 28 Oct 2020 10:41:20 -0400 Subject: [PATCH 4/7] do not add langevin thermostat forces and torques if disabled, e.g. in 2d system. Note that fix rigid/small does not support the force or torque options and thus the zeroing has to be done directly when computing the langevin data. --- src/RIGID/fix_rigid.cpp | 12 ++++++------ src/RIGID/fix_rigid_small.cpp | 5 +++++ 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/src/RIGID/fix_rigid.cpp b/src/RIGID/fix_rigid.cpp index 2161578d3d..68c44b3e26 100644 --- a/src/RIGID/fix_rigid.cpp +++ b/src/RIGID/fix_rigid.cpp @@ -1098,12 +1098,12 @@ void FixRigid::compute_forces_and_torques() // include Langevin thermostat forces for (ibody = 0; ibody < nbody; ibody++) { - fcm[ibody][0] = all[ibody][0] + langextra[ibody][0]; - fcm[ibody][1] = all[ibody][1] + langextra[ibody][1]; - fcm[ibody][2] = all[ibody][2] + langextra[ibody][2]; - torque[ibody][0] = all[ibody][3] + langextra[ibody][3]; - torque[ibody][1] = all[ibody][4] + langextra[ibody][4]; - torque[ibody][2] = all[ibody][5] + langextra[ibody][5]; + fcm[ibody][0] = all[ibody][0] + fflag[ibody][0]*langextra[ibody][0]; + fcm[ibody][1] = all[ibody][1] + fflag[ibody][1]*langextra[ibody][1]; + fcm[ibody][2] = all[ibody][2] + fflag[ibody][2]*langextra[ibody][2]; + torque[ibody][0] = all[ibody][3] + tflag[ibody][0]*langextra[ibody][3]; + torque[ibody][1] = all[ibody][4] + tflag[ibody][1]*langextra[ibody][4]; + torque[ibody][2] = all[ibody][5] + tflag[ibody][2]*langextra[ibody][5]; } // add gravity force to COM of each body diff --git a/src/RIGID/fix_rigid_small.cpp b/src/RIGID/fix_rigid_small.cpp index 650a1d9fc3..e867e5bb68 100644 --- a/src/RIGID/fix_rigid_small.cpp +++ b/src/RIGID/fix_rigid_small.cpp @@ -875,6 +875,11 @@ void FixRigidSmall::apply_langevin_thermostat() // convert langevin torques from body frame back to space frame MathExtra::matvec(ex_space,ey_space,ez_space,tbody,&langextra[ibody][3]); + + // enforce 2d motion + + if (domain->dimension == 2) + langextra[ibody][2] = langextra[ibody][3] = langextra[ibody][4] = 0.0; } } From c25ef8edb025751ae1b8d19c1a026523fc58800d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 28 Oct 2020 15:11:19 -0400 Subject: [PATCH 5/7] fix segfault: must not count bonds on atoms that are not in a molecule --- src/delete_atoms.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 03cd20947d..3dbf21ae59 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -557,6 +557,7 @@ void DeleteAtoms::recount_topology() for (int i = 0; i < nlocal; i++) { imol = molindex[i]; iatom = molatom[i]; + if (imol < 0) continue; nbonds += onemols[imol]->num_bond[iatom]; nangles += onemols[imol]->num_angle[iatom]; ndihedrals += onemols[imol]->num_dihedral[iatom]; From 9f1526c66dec2e823b2c58f11e87bcfec8abd968 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 28 Oct 2020 15:42:50 -0400 Subject: [PATCH 6/7] cannot currently use replicate command with atom style template --- src/replicate.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/replicate.cpp b/src/replicate.cpp index fb29fd63ab..7a8b5d28c2 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -43,6 +43,9 @@ void Replicate::command(int narg, char **arg) error->all(FLERR,"Replicate command before simulation box is defined"); if (narg < 3 || narg > 4) error->all(FLERR,"Illegal replicate command"); + if (atom->molecular == Atom::TEMPLATE) + error->all(FLERR,"Cannot use replicate command with atom style template"); + int me = comm->me; int nprocs = comm->nprocs; From bf87c0dc563bc41963a0ee517b6015a1460a8f45 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 28 Oct 2020 15:43:36 -0400 Subject: [PATCH 7/7] add (incomplete) unit test for atom style template --- unittest/formats/test_atom_styles.cpp | 1059 ++++++++++++++++++++++++- 1 file changed, 1058 insertions(+), 1 deletion(-) diff --git a/unittest/formats/test_atom_styles.cpp b/unittest/formats/test_atom_styles.cpp index 058d92567f..2dcefab6dd 100644 --- a/unittest/formats/test_atom_styles.cpp +++ b/unittest/formats/test_atom_styles.cpp @@ -51,10 +51,49 @@ using LAMMPS_NS::utils::split_words; +static void create_molecule_files() +{ + // create molecule files + const char h2o_file[] = "# Water molecule. SPC/E model.\n\n3 atoms\n2 bonds\n1 angles\n\n" + "Coords\n\n1 1.12456 0.09298 1.27452\n" + "2 1.53683 0.75606 1.89928\n3 0.49482 0.56390 0.65678\n\n" + "Types\n\n1 1\n2 2\n3 2\n\n" + "Charges\n\n1 -0.8472\n2 0.4236\n3 0.4236\n\n" + "Bonds\n\n1 1 1 2\n2 1 1 3\n\n" + "Angles\n\n1 1 2 1 3\n\n" + "Shake Flags\n\n1 1\n2 1\n3 1\n\n" + "Shake Atoms\n\n1 1 2 3\n2 1 2 3\n3 1 2 3\n\n" + "Shake Bond Types\n\n1 1 1 1\n2 1 1 1\n3 1 1 1\n\n" + "Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n" + "Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n"; + const char co2_file[] = "# CO2 molecule file. TraPPE model.\n\n" + "3 atoms\n2 bonds\n1 angles\n\n" + "Coords\n\n1 0.0 0.0 0.0\n2 -1.16 0.0 0.0\n3 1.16 0.0 0.0\n\n" + "Types\n\n1 1\n2 2\n3 2\n\n" + "Charges\n\n1 0.7\n2 -0.35\n3 -0.35\n\n" + "Bonds\n\n1 1 1 2\n2 1 1 3\n\n" + "Angles\n\n1 1 2 1 3\n\n" + "Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n" + "Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n"; + + FILE *fp = fopen("tmp.h2o.mol", "w"); + if (fp) { + fputs(h2o_file, fp); + fclose(fp); + } + rename("tmp.h2o.mol", "h2o.mol"); + fp = fopen("tmp.co2.mol", "w"); + if (fp) { + fputs(co2_file, fp); + fclose(fp); + } + rename("tmp.co2.mol", "co2.mol"); +} + // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; -const double EPSILON=5.0e-14; +const double EPSILON = 5.0e-14; namespace LAMMPS_NS { using ::testing::Eq; @@ -3432,6 +3471,1024 @@ TEST_F(AtomStyleTest, body_nparticle) ASSERT_EQ(bonus[3].ilocal, 6); } +TEST_F(AtomStyleTest, template) +{ + if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); + create_molecule_files(); + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); + lmp->input->one("atom_style template twomols"); + lmp->input->one("newton on"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + EXPECT_THAT(std::string(lmp->atom->atom_style), Eq("template")); + EXPECT_NE(lmp->atom->avec, nullptr); + EXPECT_EQ(lmp->atom->natoms, 0); + EXPECT_EQ(lmp->atom->nlocal, 0); + EXPECT_EQ(lmp->atom->nghost, 0); + EXPECT_EQ(lmp->atom->nmax, 1); + EXPECT_EQ(lmp->atom->tag_enable, 1); + EXPECT_EQ(lmp->atom->molecular, Atom::TEMPLATE); + EXPECT_EQ(lmp->atom->nellipsoids, 0); + EXPECT_EQ(lmp->atom->nlines, 0); + EXPECT_EQ(lmp->atom->ntris, 0); + EXPECT_EQ(lmp->atom->nbodies, 0); + EXPECT_EQ(lmp->atom->nbonds, 0); + EXPECT_EQ(lmp->atom->nangles, 0); + EXPECT_EQ(lmp->atom->ndihedrals, 0); + EXPECT_EQ(lmp->atom->nimpropers, 0); + EXPECT_EQ(lmp->atom->ntypes, 0); + EXPECT_EQ(lmp->atom->nbondtypes, 2); + EXPECT_EQ(lmp->atom->nangletypes, 2); + EXPECT_EQ(lmp->atom->ndihedraltypes, 0); + EXPECT_EQ(lmp->atom->nimpropertypes, 0); + EXPECT_EQ(lmp->atom->bond_per_atom, 0); + EXPECT_EQ(lmp->atom->angle_per_atom, 0); + EXPECT_EQ(lmp->atom->dihedral_per_atom, 0); + EXPECT_EQ(lmp->atom->improper_per_atom, 0); + EXPECT_EQ(lmp->atom->extra_bond_per_atom, 0); + EXPECT_EQ(lmp->atom->extra_angle_per_atom, 0); + EXPECT_EQ(lmp->atom->extra_dihedral_per_atom, 0); + EXPECT_EQ(lmp->atom->extra_improper_per_atom, 0); + + EXPECT_EQ(lmp->atom->sphere_flag, 0); + EXPECT_EQ(lmp->atom->ellipsoid_flag, 0); + EXPECT_EQ(lmp->atom->line_flag, 0); + EXPECT_EQ(lmp->atom->tri_flag, 0); + EXPECT_EQ(lmp->atom->body_flag, 0); + EXPECT_EQ(lmp->atom->peri_flag, 0); + EXPECT_EQ(lmp->atom->electron_flag, 0); + EXPECT_EQ(lmp->atom->wavepacket_flag, 0); + EXPECT_EQ(lmp->atom->sph_flag, 0); + EXPECT_EQ(lmp->atom->molecule_flag, 1); + EXPECT_EQ(lmp->atom->molindex_flag, 0); + EXPECT_EQ(lmp->atom->molatom_flag, 0); + EXPECT_EQ(lmp->atom->q_flag, 0); + EXPECT_EQ(lmp->atom->mu_flag, 0); + EXPECT_EQ(lmp->atom->rmass_flag, 0); + EXPECT_EQ(lmp->atom->radius_flag, 0); + EXPECT_EQ(lmp->atom->omega_flag, 0); + EXPECT_EQ(lmp->atom->torque_flag, 0); + EXPECT_EQ(lmp->atom->angmom_flag, 0); + EXPECT_EQ(lmp->atom->vfrac_flag, 0); + EXPECT_EQ(lmp->atom->spin_flag, 0); + EXPECT_EQ(lmp->atom->eradius_flag, 0); + EXPECT_EQ(lmp->atom->ervel_flag, 0); + EXPECT_EQ(lmp->atom->erforce_flag, 0); + EXPECT_EQ(lmp->atom->cs_flag, 0); + EXPECT_EQ(lmp->atom->csforce_flag, 0); + EXPECT_EQ(lmp->atom->vforce_flag, 0); + EXPECT_EQ(lmp->atom->ervelforce_flag, 0); + EXPECT_EQ(lmp->atom->etag_flag, 0); + EXPECT_EQ(lmp->atom->rho_flag, 0); + EXPECT_EQ(lmp->atom->esph_flag, 0); + EXPECT_EQ(lmp->atom->cv_flag, 0); + EXPECT_EQ(lmp->atom->vest_flag, 0); + EXPECT_EQ(lmp->atom->dpd_flag, 0); + EXPECT_EQ(lmp->atom->edpd_flag, 0); + EXPECT_EQ(lmp->atom->tdpd_flag, 0); + EXPECT_EQ(lmp->atom->mesont_flag, 0); + EXPECT_EQ(lmp->atom->sp_flag, 0); + EXPECT_EQ(lmp->atom->x0_flag, 0); + EXPECT_EQ(lmp->atom->smd_flag, 0); + EXPECT_EQ(lmp->atom->damage_flag, 0); + EXPECT_EQ(lmp->atom->contact_radius_flag, 0); + EXPECT_EQ(lmp->atom->smd_data_9_flag, 0); + EXPECT_EQ(lmp->atom->smd_stress_flag, 0); + EXPECT_EQ(lmp->atom->eff_plastic_strain_flag, 0); + EXPECT_EQ(lmp->atom->eff_plastic_strain_rate_flag, 0); + EXPECT_EQ(lmp->atom->pdscale, 1.0); + + EXPECT_NE(lmp->atom->tag, nullptr); + EXPECT_NE(lmp->atom->type, nullptr); + EXPECT_NE(lmp->atom->mask, nullptr); + EXPECT_NE(lmp->atom->image, nullptr); + EXPECT_NE(lmp->atom->x, nullptr); + EXPECT_NE(lmp->atom->v, nullptr); + EXPECT_NE(lmp->atom->f, nullptr); + EXPECT_EQ(lmp->atom->q, nullptr); + EXPECT_EQ(lmp->atom->mu, nullptr); + EXPECT_EQ(lmp->atom->omega, nullptr); + EXPECT_EQ(lmp->atom->angmom, nullptr); + EXPECT_EQ(lmp->atom->torque, nullptr); + EXPECT_EQ(lmp->atom->radius, nullptr); + EXPECT_EQ(lmp->atom->rmass, nullptr); + EXPECT_EQ(lmp->atom->ellipsoid, nullptr); + EXPECT_EQ(lmp->atom->line, nullptr); + EXPECT_EQ(lmp->atom->tri, nullptr); + EXPECT_EQ(lmp->atom->body, nullptr); + EXPECT_NE(lmp->atom->molecule, nullptr); + EXPECT_NE(lmp->atom->molindex, nullptr); + EXPECT_NE(lmp->atom->molatom, nullptr); + EXPECT_EQ(lmp->atom->num_bond, nullptr); + EXPECT_EQ(lmp->atom->bond_type, nullptr); + EXPECT_EQ(lmp->atom->bond_atom, nullptr); + EXPECT_EQ(lmp->atom->num_angle, nullptr); + EXPECT_EQ(lmp->atom->angle_type, nullptr); + EXPECT_EQ(lmp->atom->angle_atom1, nullptr); + EXPECT_EQ(lmp->atom->angle_atom2, nullptr); + EXPECT_EQ(lmp->atom->angle_atom3, nullptr); + EXPECT_EQ(lmp->atom->num_dihedral, nullptr); + EXPECT_EQ(lmp->atom->dihedral_type, nullptr); + EXPECT_EQ(lmp->atom->dihedral_atom1, nullptr); + EXPECT_EQ(lmp->atom->dihedral_atom2, nullptr); + EXPECT_EQ(lmp->atom->dihedral_atom3, nullptr); + EXPECT_EQ(lmp->atom->dihedral_atom4, nullptr); + EXPECT_EQ(lmp->atom->num_improper, nullptr); + EXPECT_EQ(lmp->atom->improper_type, nullptr); + EXPECT_EQ(lmp->atom->improper_atom1, nullptr); + EXPECT_EQ(lmp->atom->improper_atom2, nullptr); + EXPECT_EQ(lmp->atom->improper_atom3, nullptr); + EXPECT_EQ(lmp->atom->improper_atom4, nullptr); + EXPECT_EQ(lmp->atom->maxspecial, 1); + EXPECT_EQ(lmp->atom->nspecial, nullptr); + EXPECT_EQ(lmp->atom->special, nullptr); + EXPECT_EQ(lmp->atom->vfrac, nullptr); + EXPECT_EQ(lmp->atom->s0, nullptr); + EXPECT_EQ(lmp->atom->x0, nullptr); + EXPECT_EQ(lmp->atom->sp, nullptr); + EXPECT_EQ(lmp->atom->fm, nullptr); + EXPECT_EQ(lmp->atom->fm_long, nullptr); + EXPECT_EQ(lmp->atom->spin, nullptr); + EXPECT_EQ(lmp->atom->eradius, nullptr); + EXPECT_EQ(lmp->atom->ervel, nullptr); + EXPECT_EQ(lmp->atom->erforce, nullptr); + EXPECT_EQ(lmp->atom->ervelforce, nullptr); + EXPECT_EQ(lmp->atom->cs, nullptr); + EXPECT_EQ(lmp->atom->csforce, nullptr); + EXPECT_EQ(lmp->atom->vforce, nullptr); + EXPECT_EQ(lmp->atom->etag, nullptr); + EXPECT_EQ(lmp->atom->uCond, nullptr); + EXPECT_EQ(lmp->atom->uMech, nullptr); + EXPECT_EQ(lmp->atom->uChem, nullptr); + EXPECT_EQ(lmp->atom->uCG, nullptr); + EXPECT_EQ(lmp->atom->uCGnew, nullptr); + EXPECT_EQ(lmp->atom->duChem, nullptr); + EXPECT_EQ(lmp->atom->dpdTheta, nullptr); + EXPECT_EQ(lmp->atom->cc, nullptr); + EXPECT_EQ(lmp->atom->cc_flux, nullptr); + EXPECT_EQ(lmp->atom->edpd_temp, nullptr); + EXPECT_EQ(lmp->atom->edpd_flux, nullptr); + EXPECT_EQ(lmp->atom->edpd_cv, nullptr); + EXPECT_EQ(lmp->atom->length, nullptr); + EXPECT_EQ(lmp->atom->buckling, nullptr); + EXPECT_EQ(lmp->atom->bond_nt, nullptr); + EXPECT_EQ(lmp->atom->contact_radius, nullptr); + EXPECT_EQ(lmp->atom->smd_data_9, nullptr); + EXPECT_EQ(lmp->atom->smd_stress, nullptr); + EXPECT_EQ(lmp->atom->eff_plastic_strain, nullptr); + EXPECT_EQ(lmp->atom->eff_plastic_strain_rate, nullptr); + EXPECT_EQ(lmp->atom->damage, nullptr); + EXPECT_EQ(lmp->atom->rho, nullptr); + EXPECT_EQ(lmp->atom->drho, nullptr); + EXPECT_EQ(lmp->atom->esph, nullptr); + EXPECT_EQ(lmp->atom->desph, nullptr); + EXPECT_EQ(lmp->atom->cv, nullptr); + EXPECT_EQ(lmp->atom->vest, nullptr); + EXPECT_EQ(lmp->atom->nmolecule, 2); + EXPECT_NE(lmp->atom->molecules, nullptr); + EXPECT_EQ(lmp->atom->nivector, 0); + EXPECT_EQ(lmp->atom->ndvector, 0); + EXPECT_EQ(lmp->atom->iname, nullptr); + EXPECT_EQ(lmp->atom->dname, nullptr); + EXPECT_EQ(lmp->atom->mass, nullptr); + EXPECT_EQ(lmp->atom->mass_setflag, nullptr); + EXPECT_EQ(lmp->atom->nextra_grow, 0); + EXPECT_EQ(lmp->atom->nextra_restart, 0); + EXPECT_EQ(lmp->atom->nextra_border, 0); + EXPECT_EQ(lmp->atom->nextra_grow_max, 0); + EXPECT_EQ(lmp->atom->nextra_restart_max, 0); + EXPECT_EQ(lmp->atom->nextra_border_max, 0); + EXPECT_EQ(lmp->atom->nextra_store, 0); + EXPECT_EQ(lmp->atom->extra_grow, nullptr); + EXPECT_EQ(lmp->atom->extra_restart, nullptr); + EXPECT_EQ(lmp->atom->extra_border, nullptr); + EXPECT_EQ(lmp->atom->extra, nullptr); + EXPECT_EQ(lmp->atom->sametag, nullptr); + EXPECT_EQ(lmp->atom->map_style, 3); + EXPECT_EQ(lmp->atom->map_user, 0); + EXPECT_EQ(lmp->atom->map_tag_max, -1); + + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("create_box 4 box bond/types 2 angle/types 2 "); + lmp->input->one("create_atoms 0 single -2.0 2.0 0.1 mol twomols 65234"); + lmp->input->one("create_atoms 0 single -2.0 -2.0 -0.1 mol twomols 62346"); + lmp->input->one("create_atoms 0 single 2.0 2.0 -0.1 mol twomols 61354"); + lmp->input->one("create_atoms 3 single 2.0 -2.0 0.1"); + lmp->input->one("create_atoms 3 single 2.0 2.0 -2.1"); + lmp->input->one("create_atoms 4 single 2.0 -2.0 2.1"); + lmp->input->one("mass 1 16.0"); + lmp->input->one("mass 2 1.0"); + lmp->input->one("mass 3 12.0"); + lmp->input->one("mass 4 16.0"); + lmp->input->one("bond_style zero"); + lmp->input->one("bond_coeff 1 1.0"); + lmp->input->one("bond_coeff 2 1.16"); + lmp->input->one("angle_style zero"); + lmp->input->one("angle_coeff * 109.0"); + lmp->input->one("pair_coeff * *"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + EXPECT_THAT(std::string(lmp->atom->atom_style), Eq("template")); + EXPECT_NE(lmp->atom->avec, nullptr); + EXPECT_EQ(lmp->atom->natoms, 12); + EXPECT_EQ(lmp->atom->nbonds, 6); + EXPECT_EQ(lmp->atom->nbondtypes, 2); + EXPECT_EQ(lmp->atom->nangles, 3); + EXPECT_EQ(lmp->atom->nangletypes, 2); + EXPECT_EQ(lmp->atom->nellipsoids, 0); + EXPECT_EQ(lmp->atom->nlocal, 12); + EXPECT_EQ(lmp->atom->nghost, 0); + EXPECT_NE(lmp->atom->nmax, -1); + EXPECT_EQ(lmp->atom->tag_enable, 1); + EXPECT_EQ(lmp->atom->molecular, Atom::TEMPLATE); + EXPECT_EQ(lmp->atom->ntypes, 4); + EXPECT_EQ(lmp->atom->nextra_grow, 0); + EXPECT_EQ(lmp->atom->nextra_restart, 0); + EXPECT_EQ(lmp->atom->nextra_border, 0); + EXPECT_EQ(lmp->atom->nextra_grow_max, 0); + EXPECT_EQ(lmp->atom->nextra_restart_max, 0); + EXPECT_EQ(lmp->atom->nextra_border_max, 0); + EXPECT_EQ(lmp->atom->nextra_store, 0); + EXPECT_EQ(lmp->atom->extra_grow, nullptr); + EXPECT_EQ(lmp->atom->extra_restart, nullptr); + EXPECT_EQ(lmp->atom->extra_border, nullptr); + EXPECT_EQ(lmp->atom->extra, nullptr); + + EXPECT_NE(lmp->atom->mass, nullptr); + EXPECT_NE(lmp->atom->mass_setflag, nullptr); + + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("write_data test_atom_styles.data"); + lmp->input->one("clear"); + lmp->input->one("units real"); + lmp->input->one("newton off"); + lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); + lmp->input->one("atom_style template twomols"); + lmp->input->one("pair_style zero 4.0"); + lmp->input->one("bond_style zero"); + lmp->input->one("angle_style zero"); + lmp->input->one("atom_modify map array"); + lmp->input->one("read_data test_atom_styles.data"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + EXPECT_THAT(std::string(lmp->atom->atom_style), Eq("template")); + EXPECT_NE(lmp->atom->avec, nullptr); + + EXPECT_EQ(lmp->atom->natoms, 12); + EXPECT_EQ(lmp->atom->nlocal, 12); + EXPECT_EQ(lmp->atom->nbonds, 6); + EXPECT_EQ(lmp->atom->nangles, 3); + EXPECT_EQ(lmp->atom->nbondtypes, 2); + EXPECT_EQ(lmp->atom->nangletypes, 2); + EXPECT_EQ(lmp->atom->nghost, 0); + EXPECT_NE(lmp->atom->nmax, -1); + EXPECT_EQ(lmp->atom->tag_enable, 1); + EXPECT_EQ(lmp->atom->molecular, Atom::TEMPLATE); + EXPECT_EQ(lmp->atom->ntypes, 4); + EXPECT_NE(lmp->atom->sametag, nullptr); + EXPECT_EQ(lmp->atom->tag_consecutive(), 1); + EXPECT_EQ(lmp->atom->map_style, Atom::MAP_ARRAY); + EXPECT_EQ(lmp->atom->map_user, 1); + EXPECT_EQ(lmp->atom->map_tag_max, 12); + + auto molecule = lmp->atom->molecule; + auto molindex = lmp->atom->molindex; + auto molatom = lmp->atom->molatom; + + EXPECT_EQ(molecule[GETIDX(1)], 1); + EXPECT_EQ(molecule[GETIDX(2)], 1); + EXPECT_EQ(molecule[GETIDX(3)], 1); + EXPECT_EQ(molecule[GETIDX(4)], 2); + EXPECT_EQ(molecule[GETIDX(5)], 2); + EXPECT_EQ(molecule[GETIDX(6)], 2); + EXPECT_EQ(molecule[GETIDX(7)], 3); + EXPECT_EQ(molecule[GETIDX(8)], 3); + EXPECT_EQ(molecule[GETIDX(9)], 3); + EXPECT_EQ(molecule[GETIDX(10)], 0); + EXPECT_EQ(molecule[GETIDX(11)], 0); + EXPECT_EQ(molecule[GETIDX(12)], 0); + EXPECT_EQ(molindex[GETIDX(1)], 0); + EXPECT_EQ(molindex[GETIDX(2)], 0); + EXPECT_EQ(molindex[GETIDX(3)], 0); + EXPECT_EQ(molindex[GETIDX(4)], 0); + EXPECT_EQ(molindex[GETIDX(5)], 0); + EXPECT_EQ(molindex[GETIDX(6)], 0); + EXPECT_EQ(molindex[GETIDX(7)], 0); + EXPECT_EQ(molindex[GETIDX(8)], 0); + EXPECT_EQ(molindex[GETIDX(9)], 0); + EXPECT_EQ(molindex[GETIDX(10)], -1); + EXPECT_EQ(molindex[GETIDX(11)], -1); + EXPECT_EQ(molindex[GETIDX(12)], -1); + EXPECT_EQ(molatom[GETIDX(1)], 0); + EXPECT_EQ(molatom[GETIDX(2)], 1); + EXPECT_EQ(molatom[GETIDX(3)], 2); + EXPECT_EQ(molatom[GETIDX(4)], 0); + EXPECT_EQ(molatom[GETIDX(5)], 1); + EXPECT_EQ(molatom[GETIDX(6)], 2); + EXPECT_EQ(molatom[GETIDX(7)], 0); + EXPECT_EQ(molatom[GETIDX(8)], 1); + EXPECT_EQ(molatom[GETIDX(9)], 2); + EXPECT_EQ(molatom[GETIDX(10)], -1); + EXPECT_EQ(molatom[GETIDX(11)], -1); + EXPECT_EQ(molatom[GETIDX(12)], -1); + + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("clear"); + lmp->input->one("units real"); + lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); + lmp->input->one("atom_style template twomols"); + lmp->input->one("pair_style zero 4.0"); + lmp->input->one("bond_style zero"); + lmp->input->one("angle_style zero"); + lmp->input->one("atom_modify map array"); + lmp->input->one("read_data test_atom_styles.data"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + EXPECT_THAT(std::string(lmp->atom->atom_style), Eq("template")); + EXPECT_NE(lmp->atom->avec, nullptr); + + EXPECT_EQ(lmp->atom->natoms, 12); + EXPECT_EQ(lmp->atom->nlocal, 12); + EXPECT_EQ(lmp->atom->nbonds, 6); + EXPECT_EQ(lmp->atom->nangles, 3); + EXPECT_EQ(lmp->atom->nbondtypes, 2); + EXPECT_EQ(lmp->atom->nangletypes, 2); + EXPECT_EQ(lmp->atom->nghost, 0); + EXPECT_NE(lmp->atom->nmax, -1); + EXPECT_EQ(lmp->atom->tag_enable, 1); + EXPECT_EQ(lmp->atom->molecular, Atom::TEMPLATE); + EXPECT_EQ(lmp->atom->ntypes, 4); + EXPECT_NE(lmp->atom->sametag, nullptr); + EXPECT_EQ(lmp->atom->tag_consecutive(), 1); + EXPECT_EQ(lmp->atom->map_style, Atom::MAP_ARRAY); + EXPECT_EQ(lmp->atom->map_user, 1); + EXPECT_EQ(lmp->atom->map_tag_max, 12); + + molecule = lmp->atom->molecule; + molindex = lmp->atom->molindex; + molatom = lmp->atom->molatom; + + EXPECT_EQ(molindex[GETIDX(1)], 0); + EXPECT_EQ(molindex[GETIDX(2)], 0); + EXPECT_EQ(molindex[GETIDX(3)], 0); + EXPECT_EQ(molindex[GETIDX(4)], 0); + EXPECT_EQ(molindex[GETIDX(5)], 0); + EXPECT_EQ(molindex[GETIDX(6)], 0); + EXPECT_EQ(molindex[GETIDX(7)], 0); + EXPECT_EQ(molindex[GETIDX(8)], 0); + EXPECT_EQ(molindex[GETIDX(9)], 0); + EXPECT_EQ(molindex[GETIDX(10)], -1); + EXPECT_EQ(molindex[GETIDX(11)], -1); + EXPECT_EQ(molindex[GETIDX(12)], -1); + EXPECT_EQ(molatom[GETIDX(1)], 0); + EXPECT_EQ(molatom[GETIDX(2)], 1); + EXPECT_EQ(molatom[GETIDX(3)], 2); + EXPECT_EQ(molatom[GETIDX(4)], 0); + EXPECT_EQ(molatom[GETIDX(5)], 1); + EXPECT_EQ(molatom[GETIDX(6)], 2); + EXPECT_EQ(molatom[GETIDX(7)], 0); + EXPECT_EQ(molatom[GETIDX(8)], 1); + EXPECT_EQ(molatom[GETIDX(9)], 2); + EXPECT_EQ(molatom[GETIDX(10)], -1); + EXPECT_EQ(molatom[GETIDX(11)], -1); + EXPECT_EQ(molatom[GETIDX(12)], -1); + + auto x = lmp->atom->x; + auto v = lmp->atom->v; + auto type = lmp->atom->type; + + EXPECT_NEAR(x[GETIDX(10)][0], 2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(10)][1], -2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(10)][2], 0.1, EPSILON); + EXPECT_NEAR(x[GETIDX(11)][0], 2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(11)][1], 2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(11)][2], -2.1, EPSILON); + EXPECT_NEAR(x[GETIDX(12)][0], 2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(12)][1], -2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(12)][2], 2.1, EPSILON); + EXPECT_NEAR(v[GETIDX(1)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(1)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(1)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(2)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(2)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(2)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(3)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(3)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(3)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(4)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(4)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(4)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(5)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(5)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(5)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(6)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(6)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(6)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(7)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(7)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(7)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(8)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(8)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(8)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(9)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(9)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(9)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(10)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(10)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(10)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(11)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(11)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(11)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(12)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(12)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(12)][2], 0.0, EPSILON); + EXPECT_EQ(type[GETIDX(1)], 1); + EXPECT_EQ(type[GETIDX(2)], 2); + EXPECT_EQ(type[GETIDX(3)], 2); + EXPECT_EQ(type[GETIDX(4)], 1); + EXPECT_EQ(type[GETIDX(5)], 2); + EXPECT_EQ(type[GETIDX(6)], 2); + EXPECT_EQ(type[GETIDX(7)], 1); + EXPECT_EQ(type[GETIDX(8)], 2); + EXPECT_EQ(type[GETIDX(9)], 2); + EXPECT_EQ(type[GETIDX(10)], 3); + EXPECT_EQ(type[GETIDX(11)], 3); + EXPECT_EQ(type[GETIDX(12)], 4); + + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("group two id 7:10"); + lmp->input->one("delete_atoms group two compress no"); + lmp->input->one("write_restart test_atom_styles.restart"); + lmp->input->one("clear"); + lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); + lmp->input->one("read_restart test_atom_styles.restart"); + // FIXME. + // lmp->input->one("replicate 1 1 2 bbox"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + EXPECT_THAT(std::string(lmp->atom->atom_style), Eq("template")); + EXPECT_NE(lmp->atom->avec, nullptr); + EXPECT_EQ(lmp->atom->natoms, 8); + EXPECT_EQ(lmp->atom->nlocal, 8); + EXPECT_EQ(lmp->atom->nghost, 0); + EXPECT_NE(lmp->atom->nmax, -1); + EXPECT_EQ(lmp->atom->tag_enable, 1); + EXPECT_EQ(lmp->atom->q_flag, 0); + EXPECT_EQ(lmp->atom->molecular, Atom::TEMPLATE); + EXPECT_EQ(lmp->atom->ntypes, 4); + EXPECT_EQ(lmp->atom->tag_consecutive(), 0); + EXPECT_EQ(lmp->atom->map_tag_max, 12); + + type = lmp->atom->type; + molecule = lmp->atom->molecule; + molindex = lmp->atom->molindex; + molatom = lmp->atom->molatom; + EXPECT_EQ(type[GETIDX(1)], 1); + EXPECT_EQ(type[GETIDX(2)], 2); + EXPECT_EQ(type[GETIDX(3)], 2); + EXPECT_EQ(type[GETIDX(4)], 1); + EXPECT_EQ(type[GETIDX(5)], 2); + EXPECT_EQ(type[GETIDX(6)], 2); + EXPECT_EQ(type[GETIDX(11)], 3); + EXPECT_EQ(type[GETIDX(12)], 4); + + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("reset_atom_ids"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + EXPECT_EQ(lmp->atom->tag_consecutive(), 1); + EXPECT_EQ(lmp->atom->map_tag_max, 8); + + type = lmp->atom->type; + EXPECT_EQ(type[GETIDX(1)], 1); + EXPECT_EQ(type[GETIDX(2)], 2); + EXPECT_EQ(type[GETIDX(3)], 2); + EXPECT_EQ(type[GETIDX(4)], 1); + EXPECT_EQ(type[GETIDX(5)], 2); + EXPECT_EQ(type[GETIDX(6)], 2); + EXPECT_EQ(type[GETIDX(7)], 4); + EXPECT_EQ(type[GETIDX(8)], 3); +} + +TEST_F(AtomStyleTest, template_charge) +{ + if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP(); + create_molecule_files(); + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); + lmp->input->one("atom_style hybrid template twomols charge"); + lmp->input->one("newton on"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + auto hybrid = (AtomVecHybrid *)lmp->atom->avec; + ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); + ASSERT_EQ(hybrid->nstyles, 2); + ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("template")); + ASSERT_THAT(std::string(hybrid->keywords[1]), Eq("charge")); + ASSERT_NE(lmp->atom->avec, nullptr); + ASSERT_NE(hybrid->styles[0], nullptr); + ASSERT_NE(hybrid->styles[1], nullptr); + + EXPECT_EQ(lmp->atom->natoms, 0); + EXPECT_EQ(lmp->atom->nlocal, 0); + EXPECT_EQ(lmp->atom->nghost, 0); + EXPECT_EQ(lmp->atom->nmax, 1); + EXPECT_EQ(lmp->atom->tag_enable, 1); + EXPECT_EQ(lmp->atom->molecular, Atom::TEMPLATE); + EXPECT_EQ(lmp->atom->nellipsoids, 0); + EXPECT_EQ(lmp->atom->nlines, 0); + EXPECT_EQ(lmp->atom->ntris, 0); + EXPECT_EQ(lmp->atom->nbodies, 0); + EXPECT_EQ(lmp->atom->nbonds, 0); + EXPECT_EQ(lmp->atom->nangles, 0); + EXPECT_EQ(lmp->atom->ndihedrals, 0); + EXPECT_EQ(lmp->atom->nimpropers, 0); + EXPECT_EQ(lmp->atom->ntypes, 0); + EXPECT_EQ(lmp->atom->nbondtypes, 2); + EXPECT_EQ(lmp->atom->nangletypes, 2); + EXPECT_EQ(lmp->atom->ndihedraltypes, 0); + EXPECT_EQ(lmp->atom->nimpropertypes, 0); + EXPECT_EQ(lmp->atom->bond_per_atom, 0); + EXPECT_EQ(lmp->atom->angle_per_atom, 0); + EXPECT_EQ(lmp->atom->dihedral_per_atom, 0); + EXPECT_EQ(lmp->atom->improper_per_atom, 0); + EXPECT_EQ(lmp->atom->extra_bond_per_atom, 0); + EXPECT_EQ(lmp->atom->extra_angle_per_atom, 0); + EXPECT_EQ(lmp->atom->extra_dihedral_per_atom, 0); + EXPECT_EQ(lmp->atom->extra_improper_per_atom, 0); + + EXPECT_EQ(lmp->atom->sphere_flag, 0); + EXPECT_EQ(lmp->atom->ellipsoid_flag, 0); + EXPECT_EQ(lmp->atom->line_flag, 0); + EXPECT_EQ(lmp->atom->tri_flag, 0); + EXPECT_EQ(lmp->atom->body_flag, 0); + EXPECT_EQ(lmp->atom->peri_flag, 0); + EXPECT_EQ(lmp->atom->electron_flag, 0); + EXPECT_EQ(lmp->atom->wavepacket_flag, 0); + EXPECT_EQ(lmp->atom->sph_flag, 0); + EXPECT_EQ(lmp->atom->molecule_flag, 1); + EXPECT_EQ(lmp->atom->molindex_flag, 0); + EXPECT_EQ(lmp->atom->molatom_flag, 0); + EXPECT_EQ(lmp->atom->q_flag, 1); + EXPECT_EQ(lmp->atom->mu_flag, 0); + EXPECT_EQ(lmp->atom->rmass_flag, 0); + EXPECT_EQ(lmp->atom->radius_flag, 0); + EXPECT_EQ(lmp->atom->omega_flag, 0); + EXPECT_EQ(lmp->atom->torque_flag, 0); + EXPECT_EQ(lmp->atom->angmom_flag, 0); + EXPECT_EQ(lmp->atom->vfrac_flag, 0); + EXPECT_EQ(lmp->atom->spin_flag, 0); + EXPECT_EQ(lmp->atom->eradius_flag, 0); + EXPECT_EQ(lmp->atom->ervel_flag, 0); + EXPECT_EQ(lmp->atom->erforce_flag, 0); + EXPECT_EQ(lmp->atom->cs_flag, 0); + EXPECT_EQ(lmp->atom->csforce_flag, 0); + EXPECT_EQ(lmp->atom->vforce_flag, 0); + EXPECT_EQ(lmp->atom->ervelforce_flag, 0); + EXPECT_EQ(lmp->atom->etag_flag, 0); + EXPECT_EQ(lmp->atom->rho_flag, 0); + EXPECT_EQ(lmp->atom->esph_flag, 0); + EXPECT_EQ(lmp->atom->cv_flag, 0); + EXPECT_EQ(lmp->atom->vest_flag, 0); + EXPECT_EQ(lmp->atom->dpd_flag, 0); + EXPECT_EQ(lmp->atom->edpd_flag, 0); + EXPECT_EQ(lmp->atom->tdpd_flag, 0); + EXPECT_EQ(lmp->atom->mesont_flag, 0); + EXPECT_EQ(lmp->atom->sp_flag, 0); + EXPECT_EQ(lmp->atom->x0_flag, 0); + EXPECT_EQ(lmp->atom->smd_flag, 0); + EXPECT_EQ(lmp->atom->damage_flag, 0); + EXPECT_EQ(lmp->atom->contact_radius_flag, 0); + EXPECT_EQ(lmp->atom->smd_data_9_flag, 0); + EXPECT_EQ(lmp->atom->smd_stress_flag, 0); + EXPECT_EQ(lmp->atom->eff_plastic_strain_flag, 0); + EXPECT_EQ(lmp->atom->eff_plastic_strain_rate_flag, 0); + EXPECT_EQ(lmp->atom->pdscale, 1.0); + + EXPECT_NE(lmp->atom->tag, nullptr); + EXPECT_NE(lmp->atom->type, nullptr); + EXPECT_NE(lmp->atom->mask, nullptr); + EXPECT_NE(lmp->atom->image, nullptr); + EXPECT_NE(lmp->atom->x, nullptr); + EXPECT_NE(lmp->atom->v, nullptr); + EXPECT_NE(lmp->atom->f, nullptr); + EXPECT_NE(lmp->atom->q, nullptr); + EXPECT_EQ(lmp->atom->mu, nullptr); + EXPECT_EQ(lmp->atom->omega, nullptr); + EXPECT_EQ(lmp->atom->angmom, nullptr); + EXPECT_EQ(lmp->atom->torque, nullptr); + EXPECT_EQ(lmp->atom->radius, nullptr); + EXPECT_EQ(lmp->atom->rmass, nullptr); + EXPECT_EQ(lmp->atom->ellipsoid, nullptr); + EXPECT_EQ(lmp->atom->line, nullptr); + EXPECT_EQ(lmp->atom->tri, nullptr); + EXPECT_EQ(lmp->atom->body, nullptr); + EXPECT_NE(lmp->atom->molecule, nullptr); + EXPECT_NE(lmp->atom->molindex, nullptr); + EXPECT_NE(lmp->atom->molatom, nullptr); + EXPECT_EQ(lmp->atom->num_bond, nullptr); + EXPECT_EQ(lmp->atom->bond_type, nullptr); + EXPECT_EQ(lmp->atom->bond_atom, nullptr); + EXPECT_EQ(lmp->atom->num_angle, nullptr); + EXPECT_EQ(lmp->atom->angle_type, nullptr); + EXPECT_EQ(lmp->atom->angle_atom1, nullptr); + EXPECT_EQ(lmp->atom->angle_atom2, nullptr); + EXPECT_EQ(lmp->atom->angle_atom3, nullptr); + EXPECT_EQ(lmp->atom->num_dihedral, nullptr); + EXPECT_EQ(lmp->atom->dihedral_type, nullptr); + EXPECT_EQ(lmp->atom->dihedral_atom1, nullptr); + EXPECT_EQ(lmp->atom->dihedral_atom2, nullptr); + EXPECT_EQ(lmp->atom->dihedral_atom3, nullptr); + EXPECT_EQ(lmp->atom->dihedral_atom4, nullptr); + EXPECT_EQ(lmp->atom->num_improper, nullptr); + EXPECT_EQ(lmp->atom->improper_type, nullptr); + EXPECT_EQ(lmp->atom->improper_atom1, nullptr); + EXPECT_EQ(lmp->atom->improper_atom2, nullptr); + EXPECT_EQ(lmp->atom->improper_atom3, nullptr); + EXPECT_EQ(lmp->atom->improper_atom4, nullptr); + EXPECT_EQ(lmp->atom->maxspecial, 1); + EXPECT_EQ(lmp->atom->nspecial, nullptr); + EXPECT_EQ(lmp->atom->special, nullptr); + EXPECT_EQ(lmp->atom->vfrac, nullptr); + EXPECT_EQ(lmp->atom->s0, nullptr); + EXPECT_EQ(lmp->atom->x0, nullptr); + EXPECT_EQ(lmp->atom->sp, nullptr); + EXPECT_EQ(lmp->atom->fm, nullptr); + EXPECT_EQ(lmp->atom->fm_long, nullptr); + EXPECT_EQ(lmp->atom->spin, nullptr); + EXPECT_EQ(lmp->atom->eradius, nullptr); + EXPECT_EQ(lmp->atom->ervel, nullptr); + EXPECT_EQ(lmp->atom->erforce, nullptr); + EXPECT_EQ(lmp->atom->ervelforce, nullptr); + EXPECT_EQ(lmp->atom->cs, nullptr); + EXPECT_EQ(lmp->atom->csforce, nullptr); + EXPECT_EQ(lmp->atom->vforce, nullptr); + EXPECT_EQ(lmp->atom->etag, nullptr); + EXPECT_EQ(lmp->atom->uCond, nullptr); + EXPECT_EQ(lmp->atom->uMech, nullptr); + EXPECT_EQ(lmp->atom->uChem, nullptr); + EXPECT_EQ(lmp->atom->uCG, nullptr); + EXPECT_EQ(lmp->atom->uCGnew, nullptr); + EXPECT_EQ(lmp->atom->duChem, nullptr); + EXPECT_EQ(lmp->atom->dpdTheta, nullptr); + EXPECT_EQ(lmp->atom->cc, nullptr); + EXPECT_EQ(lmp->atom->cc_flux, nullptr); + EXPECT_EQ(lmp->atom->edpd_temp, nullptr); + EXPECT_EQ(lmp->atom->edpd_flux, nullptr); + EXPECT_EQ(lmp->atom->edpd_cv, nullptr); + EXPECT_EQ(lmp->atom->length, nullptr); + EXPECT_EQ(lmp->atom->buckling, nullptr); + EXPECT_EQ(lmp->atom->bond_nt, nullptr); + EXPECT_EQ(lmp->atom->contact_radius, nullptr); + EXPECT_EQ(lmp->atom->smd_data_9, nullptr); + EXPECT_EQ(lmp->atom->smd_stress, nullptr); + EXPECT_EQ(lmp->atom->eff_plastic_strain, nullptr); + EXPECT_EQ(lmp->atom->eff_plastic_strain_rate, nullptr); + EXPECT_EQ(lmp->atom->damage, nullptr); + EXPECT_EQ(lmp->atom->rho, nullptr); + EXPECT_EQ(lmp->atom->drho, nullptr); + EXPECT_EQ(lmp->atom->esph, nullptr); + EXPECT_EQ(lmp->atom->desph, nullptr); + EXPECT_EQ(lmp->atom->cv, nullptr); + EXPECT_EQ(lmp->atom->vest, nullptr); + EXPECT_EQ(lmp->atom->nmolecule, 2); + EXPECT_NE(lmp->atom->molecules, nullptr); + EXPECT_EQ(lmp->atom->nivector, 0); + EXPECT_EQ(lmp->atom->ndvector, 0); + EXPECT_EQ(lmp->atom->iname, nullptr); + EXPECT_EQ(lmp->atom->dname, nullptr); + EXPECT_EQ(lmp->atom->mass, nullptr); + EXPECT_EQ(lmp->atom->mass_setflag, nullptr); + EXPECT_EQ(lmp->atom->nextra_grow, 0); + EXPECT_EQ(lmp->atom->nextra_restart, 0); + EXPECT_EQ(lmp->atom->nextra_border, 0); + EXPECT_EQ(lmp->atom->nextra_grow_max, 0); + EXPECT_EQ(lmp->atom->nextra_restart_max, 0); + EXPECT_EQ(lmp->atom->nextra_border_max, 0); + EXPECT_EQ(lmp->atom->nextra_store, 0); + EXPECT_EQ(lmp->atom->extra_grow, nullptr); + EXPECT_EQ(lmp->atom->extra_restart, nullptr); + EXPECT_EQ(lmp->atom->extra_border, nullptr); + EXPECT_EQ(lmp->atom->extra, nullptr); + EXPECT_EQ(lmp->atom->sametag, nullptr); + EXPECT_EQ(lmp->atom->map_style, 3); + EXPECT_EQ(lmp->atom->map_user, 0); + EXPECT_EQ(lmp->atom->map_tag_max, -1); + + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("create_box 4 box bond/types 2 angle/types 2 "); + lmp->input->one("create_atoms 0 single -2.0 2.0 0.1 mol twomols 65234"); + lmp->input->one("create_atoms 0 single -2.0 -2.0 -0.1 mol twomols 62346"); + lmp->input->one("create_atoms 0 single 2.0 2.0 -0.1 mol twomols 61354"); + lmp->input->one("create_atoms 3 single 2.0 -2.0 0.1"); + lmp->input->one("create_atoms 3 single 2.0 2.0 -2.1"); + lmp->input->one("create_atoms 4 single 2.0 -2.0 2.1"); + lmp->input->one("mass 1 16.0"); + lmp->input->one("mass 2 1.0"); + lmp->input->one("mass 3 12.0"); + lmp->input->one("mass 4 16.0"); + lmp->input->one("set atom 10 charge 0.7"); + lmp->input->one("set atom 11 charge -0.35"); + lmp->input->one("set atom 12 charge -0.35"); + lmp->input->one("bond_style zero"); + lmp->input->one("bond_coeff 1 1.0"); + lmp->input->one("bond_coeff 2 1.16"); + lmp->input->one("angle_style zero"); + lmp->input->one("angle_coeff * 109.0"); + lmp->input->one("pair_coeff * *"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + ASSERT_NE(lmp->atom->avec, nullptr); + hybrid = (AtomVecHybrid *)lmp->atom->avec; + ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); + ASSERT_EQ(hybrid->nstyles, 2); + ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("template")); + ASSERT_THAT(std::string(hybrid->keywords[1]), Eq("charge")); + ASSERT_NE(hybrid->styles[0], nullptr); + ASSERT_NE(hybrid->styles[1], nullptr); + + EXPECT_EQ(lmp->atom->natoms, 12); + EXPECT_EQ(lmp->atom->nbonds, 6); + EXPECT_EQ(lmp->atom->nbondtypes, 2); + EXPECT_EQ(lmp->atom->nangles, 3); + EXPECT_EQ(lmp->atom->nangletypes, 2); + EXPECT_EQ(lmp->atom->nellipsoids, 0); + EXPECT_EQ(lmp->atom->nlocal, 12); + EXPECT_EQ(lmp->atom->nghost, 0); + EXPECT_NE(lmp->atom->nmax, -1); + EXPECT_EQ(lmp->atom->tag_enable, 1); + EXPECT_EQ(lmp->atom->molecular, Atom::TEMPLATE); + EXPECT_EQ(lmp->atom->q_flag, 1); + EXPECT_EQ(lmp->atom->ntypes, 4); + EXPECT_EQ(lmp->atom->nextra_grow, 0); + EXPECT_EQ(lmp->atom->nextra_restart, 0); + EXPECT_EQ(lmp->atom->nextra_border, 0); + EXPECT_EQ(lmp->atom->nextra_grow_max, 0); + EXPECT_EQ(lmp->atom->nextra_restart_max, 0); + EXPECT_EQ(lmp->atom->nextra_border_max, 0); + EXPECT_EQ(lmp->atom->nextra_store, 0); + EXPECT_EQ(lmp->atom->extra_grow, nullptr); + EXPECT_EQ(lmp->atom->extra_restart, nullptr); + EXPECT_EQ(lmp->atom->extra_border, nullptr); + EXPECT_EQ(lmp->atom->extra, nullptr); + + EXPECT_NE(lmp->atom->mass, nullptr); + EXPECT_NE(lmp->atom->mass_setflag, nullptr); + + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("write_data test_atom_styles.data"); + lmp->input->one("clear"); + lmp->input->one("units real"); + lmp->input->one("newton off"); + lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); + lmp->input->one("atom_style hybrid template twomols charge"); + lmp->input->one("pair_style zero 4.0"); + lmp->input->one("bond_style zero"); + lmp->input->one("angle_style zero"); + lmp->input->one("atom_modify map array"); + lmp->input->one("read_data test_atom_styles.data"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + EXPECT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); + EXPECT_NE(lmp->atom->avec, nullptr); + + EXPECT_EQ(lmp->atom->natoms, 12); + EXPECT_EQ(lmp->atom->nlocal, 12); + EXPECT_EQ(lmp->atom->nbonds, 6); + EXPECT_EQ(lmp->atom->nangles, 3); + EXPECT_EQ(lmp->atom->nbondtypes, 2); + EXPECT_EQ(lmp->atom->nangletypes, 2); + EXPECT_EQ(lmp->atom->nghost, 0); + EXPECT_NE(lmp->atom->nmax, -1); + EXPECT_EQ(lmp->atom->tag_enable, 1); + EXPECT_EQ(lmp->atom->molecular, Atom::TEMPLATE); + EXPECT_EQ(lmp->atom->ntypes, 4); + EXPECT_NE(lmp->atom->sametag, nullptr); + EXPECT_EQ(lmp->atom->tag_consecutive(), 1); + EXPECT_EQ(lmp->atom->map_style, Atom::MAP_ARRAY); + EXPECT_EQ(lmp->atom->map_user, 1); + EXPECT_EQ(lmp->atom->map_tag_max, 12); + + auto molecule = lmp->atom->molecule; + auto molindex = lmp->atom->molindex; + auto molatom = lmp->atom->molatom; + + EXPECT_EQ(molecule[GETIDX(1)], 1); + EXPECT_EQ(molecule[GETIDX(2)], 1); + EXPECT_EQ(molecule[GETIDX(3)], 1); + EXPECT_EQ(molecule[GETIDX(4)], 2); + EXPECT_EQ(molecule[GETIDX(5)], 2); + EXPECT_EQ(molecule[GETIDX(6)], 2); + EXPECT_EQ(molecule[GETIDX(7)], 3); + EXPECT_EQ(molecule[GETIDX(8)], 3); + EXPECT_EQ(molecule[GETIDX(9)], 3); + EXPECT_EQ(molecule[GETIDX(10)], 0); + EXPECT_EQ(molecule[GETIDX(11)], 0); + EXPECT_EQ(molecule[GETIDX(12)], 0); + EXPECT_EQ(molindex[GETIDX(1)], 0); + EXPECT_EQ(molindex[GETIDX(2)], 0); + EXPECT_EQ(molindex[GETIDX(3)], 0); + EXPECT_EQ(molindex[GETIDX(4)], 0); + EXPECT_EQ(molindex[GETIDX(5)], 0); + EXPECT_EQ(molindex[GETIDX(6)], 0); + EXPECT_EQ(molindex[GETIDX(7)], 0); + EXPECT_EQ(molindex[GETIDX(8)], 0); + EXPECT_EQ(molindex[GETIDX(9)], 0); + EXPECT_EQ(molindex[GETIDX(10)], -1); + EXPECT_EQ(molindex[GETIDX(11)], -1); + EXPECT_EQ(molindex[GETIDX(12)], -1); + EXPECT_EQ(molatom[GETIDX(1)], 0); + EXPECT_EQ(molatom[GETIDX(2)], 1); + EXPECT_EQ(molatom[GETIDX(3)], 2); + EXPECT_EQ(molatom[GETIDX(4)], 0); + EXPECT_EQ(molatom[GETIDX(5)], 1); + EXPECT_EQ(molatom[GETIDX(6)], 2); + EXPECT_EQ(molatom[GETIDX(7)], 0); + EXPECT_EQ(molatom[GETIDX(8)], 1); + EXPECT_EQ(molatom[GETIDX(9)], 2); + EXPECT_EQ(molatom[GETIDX(10)], -1); + EXPECT_EQ(molatom[GETIDX(11)], -1); + EXPECT_EQ(molatom[GETIDX(12)], -1); + + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("clear"); + lmp->input->one("units real"); + lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); + lmp->input->one("atom_style hybrid template twomols charge"); + lmp->input->one("pair_style zero 4.0"); + lmp->input->one("bond_style zero"); + lmp->input->one("angle_style zero"); + lmp->input->one("atom_modify map array"); + lmp->input->one("read_data test_atom_styles.data"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + EXPECT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); + EXPECT_NE(lmp->atom->avec, nullptr); + + EXPECT_EQ(lmp->atom->natoms, 12); + EXPECT_EQ(lmp->atom->nlocal, 12); + EXPECT_EQ(lmp->atom->nbonds, 6); + EXPECT_EQ(lmp->atom->nangles, 3); + EXPECT_EQ(lmp->atom->nbondtypes, 2); + EXPECT_EQ(lmp->atom->nangletypes, 2); + EXPECT_EQ(lmp->atom->nghost, 0); + EXPECT_NE(lmp->atom->nmax, -1); + EXPECT_EQ(lmp->atom->tag_enable, 1); + EXPECT_EQ(lmp->atom->molecular, Atom::TEMPLATE); + EXPECT_EQ(lmp->atom->ntypes, 4); + EXPECT_NE(lmp->atom->sametag, nullptr); + EXPECT_EQ(lmp->atom->tag_consecutive(), 1); + EXPECT_EQ(lmp->atom->map_style, Atom::MAP_ARRAY); + EXPECT_EQ(lmp->atom->map_user, 1); + EXPECT_EQ(lmp->atom->map_tag_max, 12); + + molecule = lmp->atom->molecule; + molindex = lmp->atom->molindex; + molatom = lmp->atom->molatom; + + EXPECT_EQ(molindex[GETIDX(1)], 0); + EXPECT_EQ(molindex[GETIDX(2)], 0); + EXPECT_EQ(molindex[GETIDX(3)], 0); + EXPECT_EQ(molindex[GETIDX(4)], 0); + EXPECT_EQ(molindex[GETIDX(5)], 0); + EXPECT_EQ(molindex[GETIDX(6)], 0); + EXPECT_EQ(molindex[GETIDX(7)], 0); + EXPECT_EQ(molindex[GETIDX(8)], 0); + EXPECT_EQ(molindex[GETIDX(9)], 0); + EXPECT_EQ(molindex[GETIDX(10)], -1); + EXPECT_EQ(molindex[GETIDX(11)], -1); + EXPECT_EQ(molindex[GETIDX(12)], -1); + EXPECT_EQ(molatom[GETIDX(1)], 0); + EXPECT_EQ(molatom[GETIDX(2)], 1); + EXPECT_EQ(molatom[GETIDX(3)], 2); + EXPECT_EQ(molatom[GETIDX(4)], 0); + EXPECT_EQ(molatom[GETIDX(5)], 1); + EXPECT_EQ(molatom[GETIDX(6)], 2); + EXPECT_EQ(molatom[GETIDX(7)], 0); + EXPECT_EQ(molatom[GETIDX(8)], 1); + EXPECT_EQ(molatom[GETIDX(9)], 2); + EXPECT_EQ(molatom[GETIDX(10)], -1); + EXPECT_EQ(molatom[GETIDX(11)], -1); + EXPECT_EQ(molatom[GETIDX(12)], -1); + + auto x = lmp->atom->x; + auto v = lmp->atom->v; + auto type = lmp->atom->type; + auto q = lmp->atom->q; + + EXPECT_NEAR(x[GETIDX(10)][0], 2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(10)][1], -2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(10)][2], 0.1, EPSILON); + EXPECT_NEAR(x[GETIDX(11)][0], 2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(11)][1], 2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(11)][2], -2.1, EPSILON); + EXPECT_NEAR(x[GETIDX(12)][0], 2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(12)][1], -2.0, EPSILON); + EXPECT_NEAR(x[GETIDX(12)][2], 2.1, EPSILON); + EXPECT_NEAR(v[GETIDX(1)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(1)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(1)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(2)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(2)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(2)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(3)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(3)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(3)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(4)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(4)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(4)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(5)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(5)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(5)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(6)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(6)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(6)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(7)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(7)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(7)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(8)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(8)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(8)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(9)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(9)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(9)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(10)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(10)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(10)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(11)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(11)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(11)][2], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(12)][0], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(12)][1], 0.0, EPSILON); + EXPECT_NEAR(v[GETIDX(12)][2], 0.0, EPSILON); + EXPECT_NEAR(q[GETIDX(1)], -0.8472, EPSILON); + EXPECT_NEAR(q[GETIDX(2)], 0.4236, EPSILON); + EXPECT_NEAR(q[GETIDX(3)], 0.4236, EPSILON); + EXPECT_NEAR(q[GETIDX(4)], -0.8472, EPSILON); + EXPECT_NEAR(q[GETIDX(5)], 0.4236, EPSILON); + EXPECT_NEAR(q[GETIDX(6)], 0.4236, EPSILON); + EXPECT_NEAR(q[GETIDX(7)], -0.8472, EPSILON); + EXPECT_NEAR(q[GETIDX(8)], 0.4236, EPSILON); + EXPECT_NEAR(q[GETIDX(9)], 0.4236, EPSILON); + EXPECT_NEAR(q[GETIDX(10)], 0.7, EPSILON); + EXPECT_NEAR(q[GETIDX(11)], -0.35, EPSILON); + EXPECT_NEAR(q[GETIDX(12)], -0.35, EPSILON); + EXPECT_EQ(type[GETIDX(1)], 1); + EXPECT_EQ(type[GETIDX(2)], 2); + EXPECT_EQ(type[GETIDX(3)], 2); + EXPECT_EQ(type[GETIDX(4)], 1); + EXPECT_EQ(type[GETIDX(5)], 2); + EXPECT_EQ(type[GETIDX(6)], 2); + EXPECT_EQ(type[GETIDX(7)], 1); + EXPECT_EQ(type[GETIDX(8)], 2); + EXPECT_EQ(type[GETIDX(9)], 2); + EXPECT_EQ(type[GETIDX(10)], 3); + EXPECT_EQ(type[GETIDX(11)], 3); + EXPECT_EQ(type[GETIDX(12)], 4); + + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("group two id 7:10"); + lmp->input->one("delete_atoms group two compress no"); + lmp->input->one("write_restart test_atom_styles.restart"); + lmp->input->one("clear"); + lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); + lmp->input->one("read_restart test_atom_styles.restart"); + // FIXME. + // lmp->input->one("replicate 1 1 2 bbox"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + EXPECT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid")); + EXPECT_NE(lmp->atom->avec, nullptr); + EXPECT_EQ(lmp->atom->natoms, 8); + EXPECT_EQ(lmp->atom->nlocal, 8); + EXPECT_EQ(lmp->atom->nghost, 0); + EXPECT_NE(lmp->atom->nmax, -1); + EXPECT_EQ(lmp->atom->tag_enable, 1); + EXPECT_EQ(lmp->atom->molecular, Atom::TEMPLATE); + EXPECT_EQ(lmp->atom->ntypes, 4); + EXPECT_EQ(lmp->atom->tag_consecutive(), 0); + EXPECT_EQ(lmp->atom->map_tag_max, 12); + + type = lmp->atom->type; + molecule = lmp->atom->molecule; + molindex = lmp->atom->molindex; + molatom = lmp->atom->molatom; + EXPECT_EQ(type[GETIDX(1)], 1); + EXPECT_EQ(type[GETIDX(2)], 2); + EXPECT_EQ(type[GETIDX(3)], 2); + EXPECT_EQ(type[GETIDX(4)], 1); + EXPECT_EQ(type[GETIDX(5)], 2); + EXPECT_EQ(type[GETIDX(6)], 2); + EXPECT_EQ(type[GETIDX(11)], 3); + EXPECT_EQ(type[GETIDX(12)], 4); + + if (!verbose) ::testing::internal::CaptureStdout(); + lmp->input->one("reset_atom_ids"); + if (!verbose) ::testing::internal::GetCapturedStdout(); + EXPECT_EQ(lmp->atom->tag_consecutive(), 1); + EXPECT_EQ(lmp->atom->map_tag_max, 8); + + type = lmp->atom->type; + EXPECT_EQ(type[GETIDX(1)], 1); + EXPECT_EQ(type[GETIDX(2)], 2); + EXPECT_EQ(type[GETIDX(3)], 2); + EXPECT_EQ(type[GETIDX(4)], 1); + EXPECT_EQ(type[GETIDX(5)], 2); + EXPECT_EQ(type[GETIDX(6)], 2); + EXPECT_EQ(type[GETIDX(7)], 4); + EXPECT_EQ(type[GETIDX(8)], 3); +} + TEST_F(AtomStyleTest, bond) { if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP();