Merge branch 'ROMFPMD' into rho-rom

examples/2-pyridone/2-pyridone.cfg

@@ -1,5 +1,6 @@
 verbosity=1
 xcFunctional=PBE
+FDtype=4th
 [Mesh]
 nx=128
 ny=128
@@ -12,30 +13,17 @@ lx=24.
 ly=24.
 lz=12.
 [Potentials]
-pseudopotential=pseudo.N_soft_pbe
-pseudopotential=pseudo.O_pbe
-pseudopotential=pseudo.C_pbe
-pseudopotential=pseudo.H_pbe
-[Poisson]
-solver=MG
-max_steps_initial=10
-max_steps=10
-bcx=periodic
-bcy=periodic
-bcz=periodic
+pseudopotential=pseudo.N_ONCV_PBE_SG15
+pseudopotential=pseudo.O_ONCV_PBE_SG15
+pseudopotential=pseudo.C_ONCV_PBE_SG15
+pseudopotential=pseudo.H_ONCV_PBE_SG15
 [Run]
 type=QUENCH
 [Quench]
-step_length=1.5
 max_steps=200
 atol=1.e-7
-num_lin_iterations=2
-ortho_freq=20
-interval_print_residual=10
 [Orbitals]
 initial_type=Gaussian
 initial_width=1.5
-[ProjectedMatrices]
-solver=exact
-[Restart]
-output_type=single_file
+[Poisson]
+FDtype=4th

examples/2-pyridone/README

@@ -1,6 +1,6 @@
-ln -s ../../potentials/pseudo.N_soft_pbe
-ln -s ../../potentials/pseudo.O_pbe
-ln -s ../../potentials/pseudo.C_pbe
-ln -s ../../potentials/pseudo.H_pbe
+ln -s ../../potentials/pseudo.N_ONCV_PBE_SG15
+ln -s ../../potentials/pseudo.O_ONCV_PBE_SG15
+ln -s ../../potentials/pseudo.C_ONCV_PBE_SG15
+ln -s ../../potentials/pseudo.H_ONCV_PBE_SG15
 
-srun -ppdebug -n32 /nfs/tmp2/jeanluc/SVN/MGmol/mgmol/branches/bin/mgmol-pel -c 2-pyridone.cfg -l lrs.in -i coords.in
+srun -ppdebug -n32 mgmol-opt -c 2-pyridone.cfg -l lrs.in -i coords.in

examples/2-pyridone/coords.in

@@ -1,13 +1,12 @@
-N1	1	10.0818    7.9149   6.    1
-O1	2	14.2787    7.9126   6.    1
-C1	3	 7.9625    9.1867   6.    0
-C2	3	 7.8388   11.8070   6.    0
-C3	3	10.1050   13.1610   6.    0
-C4	3	12.3830   11.8680   6.    0
-C5	3	12.2810    9.2255   6.    0
-H1	4	 6.2219    8.0878   6.    1
-H2	4	 6.0028   12.7142   6.    1
-H3	4	10.0754   15.2192   6.    1
-H4	4	14.2295   12.7482   6.    1
-H5	4	10.2332    6.0038   6.    1
-
+N1	1	10.0818    7.9149   6.
+O1	2	14.2787    7.9126   6.
+C1	3	 7.9625    9.1867   6.
+C2	3	 7.8388   11.8070   6.
+C3	3	10.1050   13.1610   6.
+C4	3	12.3830   11.8680   6.
+C5	3	12.2810    9.2255   6.
+H1	4	 6.2219    8.0878   6.
+H2	4	 6.0028   12.7142   6.
+H3	4	10.0754   15.2192   6.
+H4	4	14.2295   12.7482   6.
+H5	4	10.2332    6.0038   6.

examples/Li2GTH/README

@@ -0,0 +1,11 @@
+#Run MGmol
+mpirun -np 4 mgmol-opt -c davidson.cfg -i li2.xyz > davidson.out
+
+#extract visit files from HDF5 file
+python read_hdf5.py -bov li2.h5 Vtotal
+
+python read_hdf5.py -bov li2.h50 Function0002
+
+Note: the eigenfunctions corresponding to the 3 occupied states are stored
+in functions 2, 3 and 4 because they are the result of diagonalizing the DM
+in Davidson algorithm, not H.

examples/Li2GTH/davidson.cfg

@@ -0,0 +1,46 @@
+verbosity=2
+xcFunctional=PBE
+FDtype=4th
+[Mesh]
+nx=96
+ny=96
+nz=96
+[Domain]
+ox=-9.
+oy=-9.
+oz=-9.
+lx=18.
+ly=18.
+lz=18.
+[Potentials]
+pseudopotential=pseudo.Li_GTH_PBE
+[Poisson]
+solver=CG
+bcx=0
+bcy=0
+bcz=0
+[Run]
+type=QUENCH
+[Quench]
+solver=Davidson
+max_steps=200
+atol=1.e-8
+preconditioner_num_levels=3
+[Orbitals]
+nempty=2
+initial_type=random
+temperature=300.
+bcx=0
+bcy=0
+bcz=0
+[ProjectedMatrices]
+solver=exact
+[DensityMatrix]
+nb_inner_it=1
+mixing=1.
+[Restart]
+output_level=3
+output_filename=li2.h5
+output_type=single_file
+[Coloring]
+scope=global

examples/Li2GTH/li2.xyz

@@ -0,0 +1,4 @@
+2
+Experimental geometry (Menconi and Tozer, Chem. Phys. Lett. 2002)
+Li  1.3365 0.0 0.0
+Li -1.3365 0.0 0.0

examples/PinnedH2O/README

@@ -0,0 +1,3 @@
+Single water molecule MD, with Oxigen atom pinned to (0,0,0) coordinate:
+
+mpirun -np 4 mgmol-opt -c mgmol.cfg -i coords.in

examples/PinnedH2O/coords.in

@@ -0,0 +1,3 @@
+O1  1   0.00    0.00    0.00  0
+H1  2  -0.45    1.42   -1.07  1
+H2  2  -0.45   -1.48   -0.97  1

examples/PinnedH2O/job.basis

@@ -0,0 +1,32 @@
+#!/bin/tcsh
+#SBATCH -N 2
+#SBATCH -t 0:10:00
+#SBATCH -p pdebug
+
+date
+
+setenv OMP_NUM_THREADS 1
+#setenv KMP_DETERMINISTIC_REDUCTION 1
+
+set ncpus = 64
+
+set maindir = /p/lustre2/cheung26/mgmol-20240815
+
+setenv LD_LIBRARY_PATH ${maindir}/build_quartz/libROM/build/lib:$LD_LIBRARY_PATH
+
+set exe     = ${maindir}/build_quartz/libROM/build/examples/misc/combine_samples
+
+set snapshot_files = ""
+set increment_md_steps = 1
+set num_md_steps = 500
+
+foreach k (`seq $increment_md_steps $increment_md_steps $num_md_steps`)
+    set snapshot_files = "$snapshot_files MD_mdstep${k}_snapshot"
+end
+echo "Snapshot files: $snapshot_files"
+
+set basis_file = "PinnedH2O_orbitals_basis"
+
+srun -n $ncpus $exe -f $basis_file $snapshot_files > basis_${increment_md_steps}_${num_md_steps}_Pinned_H2O.out
+
+date

examples/PinnedH2O/job.rom

@@ -0,0 +1,35 @@
+#!/bin/tcsh
+#SBATCH -N 2
+#SBATCH -t 1:00:00
+#SBATCH -p pbatch
+
+date
+
+setenv OMP_NUM_THREADS 1
+#setenv KMP_DETERMINISTIC_REDUCTION 1
+
+set ncpus = 64
+
+set maindir = /p/lustre2/cheung26/mgmol-20240815
+
+setenv LD_LIBRARY_PATH ${maindir}/build_quartz/libROM/build/lib:$LD_LIBRARY_PATH
+
+set exe     = mgmol-opt
+
+cp $maindir/install_quartz/bin/$exe .
+
+set datadir = $maindir/examples/PinnedH2O
+
+set cfg_rom = mgmol_rom.cfg
+#cp $datadir/$cfg_rom .
+
+cp $datadir/coords.in .
+
+ln -s -f $maindir/potentials/pseudo.O_ONCV_PBE_SG15 .
+ln -s -f $maindir/potentials/pseudo.H_ONCV_PBE_SG15 .
+
+source $maindir/scripts/modules.quartz
+
+srun -n $ncpus $exe -c $cfg_rom -i coords.in > rom_PinnedH2O.out
+
+date

examples/PinnedH2O/mgmol.cfg

@@ -0,0 +1,35 @@
+verbosity=1
+xcFunctional=PBE
+FDtype=Mehrstellen
+[Mesh]
+nx=64
+ny=64
+nz=64
+[Domain]
+ox=-6.
+oy=-6.
+oz=-6.
+lx=12.
+ly=12.
+lz=12.
+[Potentials]
+pseudopotential=pseudo.O_ONCV_PBE_SG15
+pseudopotential=pseudo.H_ONCV_PBE_SG15
+[Run]
+type=MD
+[MD]
+num_steps=50
+dt=40.
+thermostat=ON
+[Thermostat]
+type=Berendsen
+temperature=1000.
+relax_time=800.
+[Quench]
+max_steps=100
+atol=1.e-8
+[Orbitals]
+initial_type=Random
+initial_width=2.
+[Restart]
+output_level=0

examples/PinnedH2O/mgmol_rom.cfg

@@ -0,0 +1,38 @@
+verbosity=1
+xcFunctional=PBE
+FDtype=Mehrstellen
+[Mesh]
+nx=64
+ny=64
+nz=64
+[Domain]
+ox=-6.
+oy=-6.
+oz=-6.
+lx=12.
+ly=12.
+lz=12.
+[Potentials]
+pseudopotential=pseudo.O_ONCV_PBE_SG15
+pseudopotential=pseudo.H_ONCV_PBE_SG15
+[Run]
+type=MD
+[MD]
+num_steps=500
+dt=40.
+thermostat=ON
+[Thermostat]
+type=Berendsen
+temperature=1000.
+relax_time=800.
+[Quench]
+max_steps=100
+atol=1.e-8
+[Orbitals]
+initial_type=Random
+initial_width=2.
+[Restart]
+output_level=4
+[ROM.offline]
+save_librom_snapshot=true
+librom_snapshot_freq=1

examples/PinnedH2O/postprocess_PinnedH2O.py

@@ -0,0 +1,27 @@
+import subprocess
+import re
+
+print("\\begin{tabular}{|c||c|c|c|c|c|c|c|}")
+print("\\hline")
+print("$k$ & $\\varepsilon = 10^{-1}$ & $\\varepsilon = 10^{-2}$ & $\\varepsilon = 10^{-3}$ & $\\varepsilon = 10^{-4}$ & $\\varepsilon = 10^{-5}$ & Snapshots \\\\")
+print("\\hline")
+
+pattern = r"For energy fraction: \d+\.\d+, take first (\d+) of \d+ basis vectors"
+for t in range(10):
+    k = 50*(t+1)
+    snapshots = 4*k
+    grep_command = f"grep 'take first' basis_1_{k}_Pinned_H2O.out"
+    result = subprocess.run(grep_command, shell=True, capture_output=True, text=True)
+    matches = re.findall(pattern, result.stdout)
+    energy_fractions = {
+        "0.9": matches[0],
+        "0.99": matches[1],
+        "0.999": matches[2],
+        "0.9999": matches[3],
+        "0.99999": matches[4],
+    }
+    line = f"{k} & {energy_fractions['0.9']} & {energy_fractions['0.99']} & {energy_fractions['0.999']} & {energy_fractions['0.9999']} & {energy_fractions['0.99999']} & {snapshots} \\\\"
+    print(line)
+
+print("\\hline")
+print("\\end{tabular}")