NOTE: routines in qmd_main are from the old routines called via nwmd.
Not used in current qmd module

== QMD TODO items ==

* Applying constraints (Rattle, Shake)
* Simulated annealing
* CPMD style dynamics
* Metadynamics

=== rough flow-chart ==
r: coordinates
g: forces
v:
m:

qmd_init
*qmd_ext_init
qmd_coords_vel(r,v,m)

qmd_gradient(g) -> * qmd_ext_gradient(r,g)

do istep_nucl =

  qmd_nucl_vel(m,v,g)  ! v update at dt/2

  qmd_nucl_post(m,r,v) ! r update at dt

  qmd_gradient(g)

  qmd_nucl_vel(m,v,g)  ! v update at dt/2

enddo

PLUMED Interface
=========
F=-gradient . Need to invert sign

# Notes on NWChem-Plumed interface

Used Plumed version 2.6

## Plumed Installation

https://www.plumed.org/doc-v2.6/user-doc/html/_installation.html

* 32bit integer BLAS/LAPACK (e.g. MKL,OpenBLAS) are required both in NWChem and Plumed.
In order to get Plumed to link the correct Blas/Lapack libraries, the variales LDFLAGS and LIBS must be supplied to
autconf.
* No need of MPI for now. It is better to disable the MPI option with --disable-mpi
Example on EMSL Tahoma
```
FC=ifort  LDFLAGS=-L$MKLROOT/lib/intel64 LIBS="-lmkl_intel_lp64 -lmkl_sequential -lmkl_core  -lpthread -lm" ./configure --prefix=/home/edo/tahoma/apps/plumed262.intel20u2 --disable-mpi
make
make install
```

## Compilation of the NWChem Interface

* modify `PATH` to point to the location of the plumed command (e.g. `/home/edo/tahoma/apps/plumed262.intel20u2/bin` in the
example above) and `LD_LIBRARY_PATH` to point to the location of the plumed libraries (e.g. `/home/edo/tahoma/apps/plumed262.intel20u2/lib` in the
example above)
* set the env. variable `USE_PLUMED=y`
* include the qmd module in `NWCHEM_MODULES`
* use BLASOPT and LAPACK_LIB compatible with the definitions used to compile Plumed.
In the example above
```
BLASOPT="-L$MKLROOT/lib/intel64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  -lpthread -lm"
LAPACK_LIB=$BLASOPT
BLAS_SIZE=4
```

## Files of the NWChem-Plumed interface

* input and output files reside in `permanent_dir`
* the Plumed input file can be either suffix.`plumed.dat` our just `plumed.dat`
* the Plumed output file will be name suffix.`plumed.out` (and its content will be copied to stdout, too)

## NWChem input options

* the keyword `ext_forces` must be added to the `qmd` input section. `ext_forces` can take an additional optional argument.
Choices are `plumed` (Plumed interface is used) or `none`.
Example:
```
....
qmd
 ext_forces
end
task dft qmd
```