Merge branch 'master' into test_intel

.github/workflows/dockerWF.yml

@@ -19,10 +19,10 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # fedora38 (gcc 13)
+        # fedora39 (gcc 13)
         # rockylinux8
         variant:
-        - fedora38
+        - fedora39
         - rocky8
     steps:
     - uses: actions/checkout@v3

.github/workflows/macWF.yml

@@ -22,7 +22,7 @@ jobs:
         variant: [ "" , "+allmodules" ]
         # see https://github.community/t/how-to-conditionally-include-exclude-items-in-matrix-eg-based-on-branch/16853/6 for possible exclusions
     env:
-      PYVERS: "py37 py38 py39 py310"
+      PYVERS: "py39 py310"
     steps:
     - uses: actions/checkout@v3
     - uses: actions/cache@v3

docker/Makefile

@@ -1,11 +1,11 @@
 
-.PHONY: ubuntu plumed2.tgz clean fedora38 rocky8
+.PHONY: ubuntu plumed2.tgz clean fedora39 rocky8
 
 ubuntu: plumed2.tgz
 	docker build -t plumed .
 
-fedora38: plumed2.tgz
-	docker build -t plumed -f fedora38 .
+fedora39: plumed2.tgz
+	docker build -t plumed -f fedora39 .
 
 rocky8: plumed2.tgz
 	docker build -t plumed -f rocky8 .

docker/fedora38 → docker/fedora39

@@ -1,4 +1,4 @@
-FROM fedora:38
+FROM fedora:39
 
 # note: at variance with centos7, here we have to explicitly install gcc
 # mdtraj 1.9.7 does not compile with python 3.11 unless installed from source

patches/qespresso-7.2.config

@@ -0,0 +1,28 @@
+
+
+function plumed_preliminary_test(){
+# check if the README.md contains the word ESPRESSO and if qe has been already configured
+  grep -q ESPRESSO  README.md 1>/dev/null 2>/dev/null && test -f make.inc 
+}
+
+function plumed_before_patch(){
+cp make.inc make.inc.plumedbck
+PWD=`pwd`
+echo "include  ${PWD}/Plumed.inc ">make.inc
+awk '{if($1=="QELIBS" && $2=="="){sub("=","= $(PLUMED_LOAD)"); print}else{print }}' make.inc.plumedbck >> make.inc
+}
+
+function plumed_after_revert(){
+  mv make.inc.plumedbck make.inc
+}
+
+function plumed_patch_info(){
+  echo ""
+  echo "For more information on Quantum Espresso you should visit http://www.quantum-espresso.org"
+  echo "To apply this patch configure Quantum Espresso by running ./configure first."
+  echo "The newer CMake installation workflow is not supported yet."
+  echo "To enable PLUMED on md runs use pw.x -plumed < md.in > md.out."
+  echo "A fixed PLUMED input file name 'plumed.dat' is used."
+  echo "This patch was kindly provided by Ralf Meyer, email: meyer.ralf(at)yahoo.com"
+}
+

patches/qespresso-7.2.diff/Modules/Makefile

@@ -0,0 +1,249 @@
+#/a Makefile for Modules
+
+include ../make.inc
+
+# location of needed modules
+MODFLAGS=$(BASEMOD_FLAGS) \
+         $(MOD_FLAG)../ELPA/src
+
+# list of modules
+
+MODULES = \
+additional_kpoints.o \
+autopilot.o \
+basic_algebra_routines.o \
+becmod.o \
+bfgs_module.o \
+bspline.o \
+bz_form.o \
+cell_base.o  \
+check_stop.o  \
+command_line_options.o \
+compute_dipole.o \
+constants.o \
+constraints_module.o \
+control_flags.o \
+coulomb_vcut.o \
+dist.o \
+electrons_base.o \
+environ_base_module.o \
+environment.o \
+extffield.o \
+fd_gradient.o \
+fft_base.o \
+fft_rho.o \
+fft_wave.o \
+fsockets.o \
+funct.o \
+generate_function.o \
+gradutils.o \
+gvecw.o \
+input_parameters.o \
+invmat.o \
+io_files.o \
+io_global.o  \
+ions_base.o \
+kind.o \
+lmdif.o \
+mdiis.o \
+mm_dispersion.o \
+mp_bands.o \
+mp_exx.o \
+mp_global.o \
+mp_images.o \
+mp_pools.o \
+mp_wave.o \
+mp_world.o \
+noncol.o \
+open_close_input_file.o \
+parameters.o \
+parser.o \
+plugin_flags.o \
+plugin_arguments.o \
+plugin_variables.o \
+pw_dot.o \
+qmmm.o \
+random_numbers.o \
+read_cards.o \
+read_input.o \
+read_namelists.o \
+read_pseudo.o \
+recvec.o \
+recvec_subs.o \
+run_info.o \
+space_group.o \
+set_para_diag.o \
+set_signal.o \
+set_vdw_corr.o \
+setqf.o \
+timestep.o\
+tsvdw.o\
+mbdlib.o\
+version.o \
+wannier_gw.o\
+wannier_new.o \
+wavefunctions.o \
+ws_base.o \
+xc_vdW_DF.o \
+xc_rVV10.o \
+io_base.o \
+qes_types_module.o \
+qes_libs_module.o  \
+qes_write_module.o \
+qes_read_module.o \
+qes_reset_module.o \
+qes_init_module.o \
+qes_bcast_module.o \
+qexsd.o   \
+qexsd_copy.o   \
+qexsd_init.o   \
+qexsd_input.o \
+hdf5_qe.o\
+qeh5_module.o\
+fox_init_module.o \
+xsf.o \
+wyckoff.o \
+wypos.o \
+zvscal.o \
+wave_gauge.o \
+plumed.o
+
+# list of RISM's modules
+
+RISMLIB = \
+allocate_fft_3drism.o \
+chempot.o \
+chempot_lauerism.o \
+closure.o \
+corrdipole_laue.o \
+correctat0_vv.o \
+corrgxy0_laue.o \
+cryst_to_car_2d.o \
+data_structure_3drism.o \
+do_1drism.o \
+do_3drism.o \
+do_lauerism.o \
+eqn_1drism.o \
+eqn_3drism.o \
+eqn_lauedipole.o \
+eqn_lauegxy0.o \
+eqn_lauelong.o \
+eqn_lauerism.o \
+eqn_laueshort.o \
+eqn_lauevoid.o \
+err_rism.o \
+guess_3drism.o \
+init_1drism.o \
+init_3drism.o \
+input_1drism.o \
+input_3drism.o \
+io_rism_xml.o \
+lauefft.o \
+lauefft_subs.o \
+lj_forcefield.o \
+lj_solute.o \
+molecorr_vv.o \
+molebridge_vv.o \
+molecule_const.o \
+molecule_types.o \
+mp_rism.o \
+mp_swap_ax_rism.o \
+normalize_lauerism.o \
+plot_rism.o \
+potential_3drism.o \
+potential_esm.o \
+potential_vv.o \
+print_chempot_3drism.o \
+print_chempot_lauerism.o \
+print_chempot_vv.o \
+print_corr_vv.o \
+print_solvavg.o \
+radfft.o \
+read_mol.o \
+read_solv.o \
+recvec_3drism.o \
+rism.o \
+rism1d_facade.o \
+rism3d_facade.o \
+rms_residual.o \
+scale_fft_3drism.o \
+scale_fft_lauerism.o \
+solute.o \
+solvation_3drism.o \
+solvation_esm.o \
+solvation_force.o \
+solvation_lauerism.o \
+solvation_pbc.o \
+solvation_stress.o \
+solvavg.o \
+solvmol.o \
+summary_1drism.o \
+summary_3drism.o \
+suscept_g0.o \
+suscept_laue.o \
+suscept_laueint.o \
+suscept_vv.o \
+write_rism_type.o \
+xml_io_rism.o
+
+# list of subroutines and functions (not modules) previously found in flib/clib
+
+OBJS = \
+atom_weight.o \
+capital.o \
+cryst_to_car.o \
+expint.o \
+generate_k_along_lines.o \
+has_xml.o \
+inpfile.o \
+int_to_char.o \
+latgen.o \
+linpack.o \
+matches.o \
+plot_io.o \
+radial_gradients.o \
+rgen.o \
+recips.o \
+remove_tot_torque.o \
+sort.o \
+trimcheck.o \
+test_input_file.o \
+date_and_tim.o \
+volume.o \
+wgauss.o \
+w0gauss.o \
+w1gauss.o \
+deviatoric.o \
+customize_signals.o \
+qmmm_aux.o \
+sockets.o \
+stack.o
+
+# GPU versions of modules
+MODULES += \
+  wavefunctions_gpu.o \
+  becmod_gpu.o \
+  becmod_subs_gpu.o \
+  cuda_subroutines.o \
+  random_numbers_gpu.o
+
+TLDEPS= libfox libla libfft libutil libmbd librxc libupf
+
+all : libqemod.a
+
+libqemod.a: 	$(MODULES) $(OBJS) $(RISMLIB)
+	$(AR) $(ARFLAGS) $@ $?       
+	$(RANLIB) $@    
+
+tldeps :
+	if test -n "$(TLDEPS)" ; then \
+	( cd ../.. ; $(MAKE) $(TLDEPS) || exit 1 ) ; fi
+
+
+clean :
+	- /bin/rm -f *.o *.a *.d *.i *~ *_tmp.f90 *.mod *.L plumed.f90
+
+plumed.f90:
+	cp $(PLUMED_FORTRAN) plumed.f90
+
+include make.depend