Merge pull request #1083 from Iximiel/v2.8_qePatches

Updating QE patches for v2.8

patches/qespresso-5.0.2.diff/PW/src/plugin_forces.f90

@@ -19,19 +19,21 @@ SUBROUTINE plugin_forces()
   USE plugin_flags
   !
   USE cell_base,        ONLY : alat, at
-  USE ions_base,        ONLY : tau, nat,amass
+  USE ions_base,        ONLY : tau, nat, amass, ityp
   USE force_mod,        ONLY : force,sigma
   USE control_flags,    ONLY : istep
   USE ener,             ONLY : etot 
   !
   IMPLICIT NONE
   !
-  INTEGER:: i,j
+  INTEGER:: i,j,ia
   REAL(DP) :: at_plumed(3,3)
   REAL(DP) :: virial(3,3)
   REAL(DP) :: volume
   REAL(DP), ALLOCATABLE :: tau_plumed(:,:)
+  REAL(DP) :: masses_plumed(nat)
   !
+  masses_plumed = 0.0_DP
   IF(use_plumed) then
     IF(ionode)THEN
       at_plumed=alat*at;  ! the cell, rescaled properly
@@ -44,9 +46,12 @@ SUBROUTINE plugin_forces()
              -at_plumed(1,2)*at_plumed(3,3)*at_plumed(2,1) &
              -at_plumed(1,3)*at_plumed(3,1)*at_plumed(2,2) 
       virial=-sigma*volume
-
+      ! the masses in QE are stored per type, see q-e//Modules/ions_base.f90
+      do ia=1,nat
+        masses_plumed(ia)=amass(ityp(ia))
+      end do
       CALL plumed_f_gcmd("setStep"//char(0),istep)
-      CALL plumed_f_gcmd("setMasses"//char(0),amass)
+      CALL plumed_f_gcmd("setMasses"//char(0),masses_plumed)
       CALL plumed_f_gcmd("setForces"//char(0),force)
       CALL plumed_f_gcmd("setPositions"//char(0),tau_plumed)
       CALL plumed_f_gcmd("setBox"//char(0),at_plumed)

patches/qespresso-6.2.diff/PW/src/plugin_ext_forces.f90

@@ -18,19 +18,21 @@ SUBROUTINE plugin_ext_forces()
   USE plugin_flags
   !
   USE cell_base,        ONLY : alat, at
-  USE ions_base,        ONLY : tau, nat,amass
+  USE ions_base,        ONLY : tau, nat, amass, ityp
   USE force_mod,        ONLY : force,sigma
   USE control_flags,    ONLY : istep
   USE ener,             ONLY : etot 
   !
   IMPLICIT NONE
   !
-  INTEGER:: i,j
+  INTEGER:: i,j,ia
   REAL(DP) :: at_plumed(3,3)
   REAL(DP) :: virial(3,3)
   REAL(DP) :: volume
   REAL(DP), ALLOCATABLE :: tau_plumed(:,:)
+  REAL(DP) :: masses_plumed(nat)
   !
+  masses_plumed = 0.0_DP
   IF(use_plumed) then
     IF(ionode)THEN
       at_plumed=alat*at;  ! the cell, rescaled properly
@@ -43,9 +45,12 @@ SUBROUTINE plugin_ext_forces()
              -at_plumed(1,2)*at_plumed(3,3)*at_plumed(2,1) &
              -at_plumed(1,3)*at_plumed(3,1)*at_plumed(2,2) 
       virial=-sigma*volume
-
+      ! the masses in QE are stored per type, see q-e//Modules/ions_base.f90
+      do ia=1,nat
+        masses_plumed(ia)=amass(ityp(ia))
+      end do
       CALL plumed_f_gcmd("setStep"//char(0),istep)
-      CALL plumed_f_gcmd("setMasses"//char(0),amass)
+      CALL plumed_f_gcmd("setMasses"//char(0),masses_plumed)
       CALL plumed_f_gcmd("setForces"//char(0),force)
       CALL plumed_f_gcmd("setPositions"//char(0),tau_plumed)
       CALL plumed_f_gcmd("setBox"//char(0),at_plumed)

patches/qespresso-7.0.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-7.0.diff/Modules/Makefile

@@ -0,0 +1,175 @@
+#/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 \
+environment.o \
+fd_gradient.o \
+fft_base.o \
+fft_rho.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 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 \
+set_hubbard_l.o \
+set_hubbard_n.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 libutil libla libfft librxc
+
+all : libqemod.a
+
+## The following is needed only for lapack compiled from sources
+
+dlamch.o : dlamch.f
+	$(F77) $(FFLAGS_NOOPT) -c $<
+
+libqemod.a: 	$(MODULES) $(OBJS)
+	$(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