The quantum espresso patch (Only PW)

developer-doc/mdTemplate.txt

@@ -69,6 +69,11 @@ command
 
 Now you can patch/unpatch your MD code, automatically linking PLUMED, as if it
 was an officially released interface.
+Note that the created diff file is executed as a bash script. This is
+particularly useful whenever your code, as a result of a configure, creates a
+makefile which can be remarkably different according to the architecture.
+In this case you can fiddle with some awk and sed to add the needed paths to
+PLUMED libraries.  
 
 \section language Language dependence
 
@@ -152,6 +157,11 @@ The various calls that can be used pass data and calculate the forces due to the
 plumed_cmd(plumedmain,"setStep",&step);                      // Pass a pointer to the current timestep to plumed
 / *** The way that you pass positions will depend on how they are stored in your code.  If the x, y and z position are all stored in a single array you may use:
 plumed_cmd(plumedmain,"setPositions",&pos[0][0]);            // Pass a pointer to the first element in the atomic positions array to plumed  
+                                                             // assuming they
+                                                             // are stored in
+                                                             // a
+                                                             // x1,y1,z1,x2,y2,z2 ...
+                                                             // kind of ordering
 / *** Othersize if you pass the three separate vectors of x, y and z positions using:
 plumed_cmd(plumedmain,"setPositionX",&x[0]);                 // Pass a pointer to the first element in the array of x component of the atomic positions to plumed
 plumed_cmd(plumedmain,"setPositionY",&y[0]);                 // Pass a pointer to the first element in the array of y component of the atomic positions to plumed

patches/patch.sh

@@ -12,7 +12,7 @@ Actions (choose one):
   -l, --list-engines
                     print a list of available MD engines
   -s, --save
-                    save (*)
+                    save, this needs *.preplumed files (*)
   -n NEWENGINE, --new NEWENGINE
                     create a new patch named NEWENGINE (*)
 Options:

patches/qespresso.diff

+# this is not patchable and is needed to place the right calls in the right place no mattder what
+cp make.sys make.sys.preplumed 
+PWD=`pwd`
+echo "include  ${PWD}/Plumed.inc ">make.sys
+awk '{if($1=="LIBS" && $2=="="){print $0" ${PLUMED_SHARED_LOAD} "}else{print }}' make.sys.preplumed >>make.sys
+exit
+patch -u -l -b -F 5 --suffix=.preplumed "./PW/src/plugin_initialization.f90" << \EOF_EOF
+--- ./PW/src/plugin_initialization.f90.preplumed
++++ ./PW/src/plugin_initialization.f90
+@@ -13,9 +13,50 @@
+   USE kinds,            ONLY : DP
+   USE io_files,         ONLY : tmp_dir
+   !
+   USE plugin_flags
+   !
++  USE ions_base,        ONLY : amass, ityp, nat
++  !
++  USE dynamics_module,  ONLY : dt
++  USE constants,        ONLY : au_ps
++  !
++  !
+   IMPLICIT NONE
+   !
++  INTEGER  :: na
++  INTEGER  :: plumedavailable
++  REAL*8   :: energyUnits,lengthUnits,timeUnits 
++  !
++  IF(use_plumed) then
++
++     CALL plumed_f_installed(plumedavailable)
++   
++     IF(plumedavailable<=0)THEN
++        write(stdout,*)"YOU ARE LOOKING FOR PLUMED BUT LOOKS LIKE IT IS NOT AVAILABLE: DO YOU HAVE IT IN YOUR LD_LIBRARY_PATH?" 
++        STOP 
++     ELSE 
++        IF (ionode) THEN
++
++            write(stdout,*)"  CREATING PLUMED FROM THE PROGRAM" 
++            call plumed_f_gcreate()
++            CALL plumed_f_gcmd("setRealPrecision"//char(0),8)
++            energyUnits=1312.75  ! Ry to kjoule mol 
++            lengthUnits=0.0529177249 ! bohr to nm
++            timeUnits=au_ps ! internal time to ps
++            call plumed_f_gcmd("setMDEnergyUnits"//char(0),energyUnits)
++            call plumed_f_gcmd("setMDLengthUnits"//char(0),lengthUnits)
++            call plumed_f_gcmd("setMDTimeUnits"//char(0),timeUnits)
++            call plumed_f_gcmd("setPlumedDat"//char(0),"plumed.dat"//char(0))
++            call plumed_f_gcmd("setLogFile"//char(0),"PLUMED.OUT"//char(0))
++            call plumed_f_gcmd("setNatoms"//char(0),nat)
++            call plumed_f_gcmd("setMDEngine"//char(0),"qespresso");
++            call plumed_f_gcmd("setTimestep"//char(0),dt);
++            call plumed_f_gcmd("init"//char(0),0);
++    
++        ENDIF
++     ENDIF
++  ENDIF
++  !
+   !
+ END SUBROUTINE plugin_initialization
+EOF_EOF
+patch -u -l -b -F 5 --suffix=.preplumed "./PW/src/plugin_forces.f90" << \EOF_EOF
+--- ./PW/src/plugin_forces.f90.preplumed
++++ ./PW/src/plugin_forces.f90
+@@ -16,9 +16,38 @@
+   USE kinds,            ONLY : DP
+   USE io_files,         ONLY : outdir
+   !
+   USE plugin_flags
+   !
++  USE cell_base,        ONLY : alat, at
++  USE ions_base,        ONLY : tau, nat,amass
++  USE force_mod,        ONLY : force
++  USE control_flags,    ONLY : istep
++  USE ener,             ONLY : etot 
++  !
+   IMPLICIT NONE
+   !
++  INTEGER:: i,j
++  REAL(DP) :: at_plumed(3,3)
++  REAL(DP), ALLOCATABLE :: tau_plumed(:,:)
++  !
++  IF(use_plumed) then
++    IF(ionode)THEN
++      at_plumed=alat*at;  ! the cell, rescaled properly
++      allocate(tau_plumed(3,nat))
++      tau_plumed=alat*tau
++
++      CALL plumed_f_gcmd("setMasses"//char(0),amass)
++      CALL plumed_f_gcmd("setForces"//char(0),force)
++      CALL plumed_f_gcmd("setStep"//char(0),istep)
++      CALL plumed_f_gcmd("setPositions"//char(0),tau_plumed)
++      CALL plumed_f_gcmd("setBox"//char(0),at_plumed)
++      CALL plumed_f_gcmd("setEnergy"//char(0),etot)
++      CALL plumed_f_gcmd("calc"//char(0),0)
++
++      deallocate(tau_plumed)
++    ENDIF
++    CALL mp_bcast(force, ionode_id, intra_image_comm)
++  ENDIF
++  !
+   !
+ END SUBROUTINE plugin_forces
+EOF_EOF