From da23472aaeeb9241353c1df16e8ded3a97098546 Mon Sep 17 00:00:00 2001
From: Lukas Krupcik <lukas.krupcik@vsb.cz>
Date: Mon, 12 Dec 2022 08:45:45 +0100
Subject: [PATCH] 	new file:  
 g/GROMACS/GROMACS-2020.3-foss-2020b-PLUMED-2.7.3.eb 	new file:  
 p/phonopy/phonopy-2.17.0-conda.eb 	modified:  
 q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a-ntypx=32.eb

---
 .../GROMACS-2020.3-foss-2020b-PLUMED-2.7.3.eb | 75 +++++++++++++++++++
 p/phonopy/phonopy-2.17.0-conda.eb             | 27 +++++++
 ...uantumESPRESSO-7.1-intel-2022a-ntypx=32.eb |  2 +-
 3 files changed, 103 insertions(+), 1 deletion(-)
 create mode 100644 g/GROMACS/GROMACS-2020.3-foss-2020b-PLUMED-2.7.3.eb
 create mode 100644 p/phonopy/phonopy-2.17.0-conda.eb

diff --git a/g/GROMACS/GROMACS-2020.3-foss-2020b-PLUMED-2.7.3.eb b/g/GROMACS/GROMACS-2020.3-foss-2020b-PLUMED-2.7.3.eb
new file mode 100644
index 00000000..b7798477
--- /dev/null
+++ b/g/GROMACS/GROMACS-2020.3-foss-2020b-PLUMED-2.7.3.eb
@@ -0,0 +1,75 @@
+# IT4Innovations 2022
+# JK
+
+name = 'GROMACS'
+version = '2020.3'
+local_plum_ver = '2.7.3'
+versionsuffix = '-PLUMED-%s' % local_plum_ver
+
+homepage = 'http://www.gromacs.org'
+description = """
+GROMACS is a versatile package to perform molecular dynamics,
+ i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
+
+This is a GPU enabled build, containing both MPI and threadMPI binaries.
+"""
+
+toolchain = {'name': 'foss', 'version': '2020b'}
+toolchainopts = {'openmp': True, 'usempi': True}
+
+source_urls = [
+    'https://ftp.gromacs.org/pub/gromacs/',
+    'ftp://ftp.gromacs.org/pub/gromacs/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+patches = [
+    'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch',
+    'GROMACS-2019_increase_test_timeout_for_GPU.patch',
+    'GROMACS-2020_add-missing-sync.patch',
+]
+checksums = [
+    {'gromacs-2020.3.tar.gz': '903183691132db14e55b011305db4b6f4901cc4912d2c56c131edfef18cc92a9'},
+    {'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch':
+     '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275'},
+    {'GROMACS-2019_increase_test_timeout_for_GPU.patch':
+     '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234'},
+    {'GROMACS-2020_add-missing-sync.patch': '3c9d7017422a722a960d26ad955d7a0f72a1305a6234bcb53851cc62662b96c9'},
+]
+
+builddependencies = [
+    ('CMake', '3.18.4'),
+    ('Ninja', '1.10.1'),
+    ('scikit-build', '0.11.1'),
+]
+
+dependencies = [
+    ('Python', '3.8.6'),
+    ('SciPy-bundle', '2020.11'),
+    ('networkx', '2.5'),
+]
+
+
+ignore_plumed_version_check = True
+configopts = '-DGMX_GPU_NB_CLUSTER_SIZE=4 '
+
+exts_defaultclass = 'PythonPackage'
+
+exts_default_options = {
+    'source_urls': [PYPI_SOURCE],
+    'use_pip': True,
+    'download_dep_fail': True,
+    'sanity_pip_check': True,
+}
+
+exts_list = [
+    ('gmxapi', '0.2.0', {
+        'preinstallopts': "export GMXTOOLCHAINDIR=%(installdir)s/share/cmake/gromacs_mpi && ",
+        'checksums': ['3954bf123da12fc60bcfaeed8263f5e2d3e16e5136c2bb5c8207b20fa7406788'],
+    }),
+]
+
+modextrapaths = {
+    'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
+}
+
+moduleclass = 'bio'
diff --git a/p/phonopy/phonopy-2.17.0-conda.eb b/p/phonopy/phonopy-2.17.0-conda.eb
new file mode 100644
index 00000000..3615020f
--- /dev/null
+++ b/p/phonopy/phonopy-2.17.0-conda.eb
@@ -0,0 +1,27 @@
+# IT4Innovations
+# LK 2022
+
+easyblock = "Conda"
+
+name = 'phonopy'
+version = '2.17.0'
+versionsuffix = '-conda'
+
+homepage = 'http://phonopy.sourceforge.net/phono3py/index.html'
+description = """This software calculates phonon-phonon interaction related properties"""
+
+toolchain = SYSTEM
+
+dependencies = [
+    ('Anaconda3', '2022.05'),
+]
+
+requirements = "%(namelower)s numpy scipy h5py pyyaml matplotlib-base spglib"
+channels = ['conda-forge']
+
+sanity_check_paths = {
+    'files': ['bin/phonopy'],
+    'dirs': ['bin', 'lib']
+}
+
+moduleclass = 'phys'
diff --git a/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a-ntypx=32.eb b/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a-ntypx=32.eb
index b4890bc2..c57c4590 100644
--- a/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a-ntypx=32.eb
+++ b/q/QuantumESPRESSO/QuantumESPRESSO-7.1-intel-2022a-ntypx=32.eb
@@ -11,7 +11,7 @@ for electronic-structure calculations and materials modeling at the nanoscale.
 It is based on density-functional theory, plane waves, and pseudopotentials
 (both norm-conserving and ultrasoft).
 
-This is a customized version whose ntypx parameter has changed to 32 (from default 10).
+This is a customized version whose ntypx parameter has been changed to 32 (from default 10).
 """
 
 toolchain = {'name': 'intel', 'version': '2022a'}