link plumed to arrayfire to build gpu enabled code

in particular a gpu version of SAXS is added in ISDB
this is just a SAXS collective variable implemented to run on GPU
a regtest is added. This was implemented with an old version of
arrayfire so it should be checked wheter it can be made more modern
a regtest is also added

configure.ac

@@ -264,6 +264,8 @@ PLUMED_CONFIG_ENABLE([boost_serialization],[search for boost serialization],[no]
 PLUMED_CONFIG_ENABLE([asmjit],[search for asmjit],[no])
 PLUMED_CONFIG_ENABLE([fftw],[search for fftw],[no])
 PLUMED_CONFIG_ENABLE([python],[search for python],[yes])
+PLUMED_CONFIG_ENABLE([af_ocl],[arrayfire_opencl],[search for arrayfire],[no])
+PLUMED_CONFIG_ENABLE([af_cuda],[arrayfire_cuda],[search for arrayfire],[no])
 
 AC_ARG_VAR(SOEXT,[extension of dynamic libraries (so/dylib)])
 AC_ARG_VAR(STATIC_LIBS,[variables that should be linked statically directly to MD code - configure will add here -ldl if necessary ])
@@ -735,6 +737,13 @@ import os
   fi
 fi
 
+if test $af_ocl == true ; then
+  PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afopencl])
+fi
+if test $af_cuda == true ; then
+  PLUMED_CHECK_PACKAGE([arrayfire.h],[af_is_double],[__PLUMED_HAS_ARRAYFIRE],[afcuda])
+fi
+
 # in non-debug mode, add -DNDEBUG
 if test "$debug" == false ; then
   AC_MSG_NOTICE([Release mode, adding -DNDEBUG])

regtest/isdb/rt-saxs-gpu/Makefile

+include ../../scripts/test.make

regtest/isdb/rt-saxs-gpu/colvar.reference

+#! FIELDS time saxs.q_0 saxs.q_1 saxs.q_2 saxs.q_3 saxs.q_4 saxs.q_5 saxs.q_6 saxs.q_7 saxs.q_8 saxs.q_9 saxs.q_10 saxs.q_11 saxs.q_12 saxs.q_13 saxs.q_14 saxs.exp_0 saxs.exp_1 saxs.exp_2 saxs.exp_3 saxs.exp_4 saxs.exp_5 saxs.exp_6 saxs.exp_7 saxs.exp_8 saxs.exp_9 saxs.exp_10 saxs.exp_11 saxs.exp_12 saxs.exp_13 saxs.exp_14
+ 0.000000 1.100661 0.863129 0.559587 0.317188 0.174275 0.100178 0.056937 0.028540 0.012530 0.006728 0.006786 0.008899 0.011032 0.012345 0.012590 1.090200 0.790632 0.453808 0.254737 0.154928 0.092150 0.052633 0.027656 0.012278 0.008806 0.013730 0.018004 0.019337 0.021013 0.022051

regtest/isdb/rt-saxs-gpu/colvarb.reference

+#! FIELDS time saxsb.q_0 saxsb.q_1 saxsb.q_2 saxsb.q_3 saxsb.q_4 saxsb.q_5 saxsb.q_6 saxsb.q_7 saxsb.q_8 saxsb.q_9 saxsb.q_10 saxsb.q_11 saxsb.q_12 saxsb.q_13 saxsb.q_14 saxsb.exp_0 saxsb.exp_1 saxsb.exp_2 saxsb.exp_3 saxsb.exp_4 saxsb.exp_5 saxsb.exp_6 saxsb.exp_7 saxsb.exp_8 saxsb.exp_9 saxsb.exp_10 saxsb.exp_11 saxsb.exp_12 saxsb.exp_13 saxsb.exp_14
+ 0.000000 1.100662 0.863129 0.559587 0.317188 0.174275 0.100178 0.056937 0.028540 0.012530 0.006728 0.006786 0.008899 0.011032 0.012345 0.012590 1.090200 0.790632 0.453808 0.254737 0.154928 0.092150 0.052633 0.027656 0.012278 0.008806 0.013730 0.018004 0.019337 0.021013 0.022051

regtest/isdb/rt-saxs-gpu/config

+mpiprocs=4
+type=driver
+arg="--plumed plumed.dat --timestep 0.005 --mf_pdb template.pdb"
+plumed_needs="arrayfire"

regtest/isdb/rt-saxs-gpu/plumed.dat

+MOLINFO STRUCTURE=template.pdb
+
+SAXS ...
+LABEL=saxs
+ATOMS=1-355
+ADDEXP
+SCEXP=3920000
+MARTINI
+QVALUE1=0.02 EXPINT1=1.0902
+QVALUE2=0.05 EXPINT2=0.790632
+QVALUE3=0.08 EXPINT3=0.453808
+QVALUE4=0.11 EXPINT4=0.254737
+QVALUE5=0.14 EXPINT5=0.154928
+QVALUE6=0.17 EXPINT6=0.0921503
+QVALUE7=0.2 EXPINT7=0.052633
+QVALUE8=0.23 EXPINT8=0.0276557
+QVALUE9=0.26 EXPINT9=0.0122775
+QVALUE10=0.29 EXPINT10=0.00880634
+QVALUE11=0.32 EXPINT11=0.0137301
+QVALUE12=0.35 EXPINT12=0.0180036
+QVALUE13=0.38 EXPINT13=0.0193374
+QVALUE14=0.41 EXPINT14=0.0210131
+QVALUE15=0.44 EXPINT15=0.0220506
+... SAXS
+
+SAXSGPU ...
+LABEL=saxsb
+ATOMS=1-355
+ADDEXP
+SCEXP=3920000
+MARTINI
+SPLITB=355
+QVALUE1=0.02 EXPINT1=1.0902
+QVALUE2=0.05 EXPINT2=0.790632
+QVALUE3=0.08 EXPINT3=0.453808
+QVALUE4=0.11 EXPINT4=0.254737
+QVALUE5=0.14 EXPINT5=0.154928
+QVALUE6=0.17 EXPINT6=0.0921503
+QVALUE7=0.2 EXPINT7=0.052633
+QVALUE8=0.23 EXPINT8=0.0276557
+QVALUE9=0.26 EXPINT9=0.0122775
+QVALUE10=0.29 EXPINT10=0.00880634
+QVALUE11=0.32 EXPINT11=0.0137301
+QVALUE12=0.35 EXPINT12=0.0180036
+QVALUE13=0.38 EXPINT13=0.0193374
+QVALUE14=0.41 EXPINT14=0.0210131
+QVALUE15=0.44 EXPINT15=0.0220506
+...
+
+PRINT ARG=(saxs\.q_.*),(saxs\.exp_.*) FILE=colvar STRIDE=1
+PRINT ARG=(saxsb\.q_.*),(saxsb\.exp_.*) FILE=colvarb STRIDE=1
+
+DUMPDERIVATIVES ARG=(saxs\.q_.*) FILE=forces FMT=%.4f
+DUMPDERIVATIVES ARG=(saxsb\.q_.*) FILE=forcesb FMT=%.4f
+
+ENDPLUMED