ROM offline calculations for MD snapshots

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_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}")

scripts/build_quartz_libROM.sh

@@ -55,7 +55,7 @@ make -j 16
 ### Currently libROM does not have the installation procedure,
 ### so copying binary file to installation directory will disrupt the relative path to libROM.so,
 ### causing a run-time error.
-#make install
+make install
 
 #      -DBLAS_LIBRARIES=/usr/tce/packages/mkl/mkl-2022.1.0/mkl/2022.1.0/lib/intel64/lib \
 #      -DLAPACK_LIBRARIES=/usr/tce/packages/mkl/mkl-2022.1.0/mkl/2022.1.0/lib/intel64/lib \  

src/Control.cc

@@ -2052,6 +2052,7 @@ void Control::setROMOptions(const boost::program_options::variables_map& vm)
             rom_pri_option.variable = ROMVariable::NONE;
 
         rom_pri_option.save_librom_snapshot = vm["ROM.offline.save_librom_snapshot"].as<bool>();
+        rom_pri_option.librom_snapshot_freq = vm["ROM.offline.librom_snapshot_freq"].as<int>();
 
         rom_pri_option.num_potbasis = vm["ROM.basis.number_of_potential_basis"].as<int>();
     }  // onpe0
@@ -2092,6 +2093,9 @@ void Control::syncROMOptions()
     mpirc = MPI_Bcast(&rom_pri_option.save_librom_snapshot, 1, MPI_C_BOOL, 0, comm_global_);
     bcast_check(mpirc);
 
+    mpirc = MPI_Bcast(&rom_pri_option.librom_snapshot_freq, 1, MPI_INT, 0, comm_global_);
+    bcast_check(mpirc);
+
     short rom_var = (short)static_cast<int>(rom_pri_option.variable);
     mpirc = MPI_Bcast(&rom_var, 1, MPI_SHORT, 0, comm_global_);
     bcast_check(mpirc);
@@ -2101,4 +2105,4 @@ void Control::syncROMOptions()
 
     mpirc = MPI_Bcast(&rom_pri_option.num_potbasis, 1, MPI_INT, 0, comm_global_);
     bcast_check(mpirc);
-}
+}

src/md.cc

@@ -406,6 +406,9 @@ void MGmol<OrbitalsType>::md(OrbitalsType** orbitals, Ions& ions)
     bool extrapolated_flag = true;
     if (ct.dt <= 0.) extrapolated_flag = false;
 
+    int librom_snapshot_freq = ct.getROMOptions().librom_snapshot_freq; 
+    if (librom_snapshot_freq == -1) librom_snapshot_freq = ct.md_print_freq;
+
     MDfiles md_files;
 
     // main MD iteration loop
@@ -625,21 +628,22 @@ void MGmol<OrbitalsType>::md(OrbitalsType** orbitals, Ions& ions)
                         count++;
                     }
 
+                    printWithTimeStamp("dumped restart file...", std::cout);
+                }
+
 #ifdef MGMOL_HAS_LIBROM
-                    // Save orbital snapshots
-                    if (ct.getROMOptions().save_librom_snapshot > 0)
-                    {
-                        int ierr = save_orbital_snapshot(
-                            ct.md_print_filename + "_mdstep" + std::to_string(mdstep), **orbitals);
+        // Save orbital snapshots
+        if (md_iteration_ % librom_snapshot_freq == 0
+            && ct.getROMOptions().save_librom_snapshot > 0)
+        {
+            int ierr = save_orbital_snapshot(
+                ct.md_print_filename + "_mdstep" + std::to_string(mdstep), **orbitals);
 
-                        if (ierr < 0)
-                            os_ << "WARNING md(): writing ROM snapshot data failed!!!" << std::endl;
-                    }
+            if (ierr < 0)
+                os_ << "WARNING md(): writing ROM snapshot data failed!!!" << std::endl;
+        }
 #endif
 
-                    printWithTimeStamp("dumped restart file...", std::cout);
-                }
-
         md_iterations_tm.stop();
 
     } // md loop

src/read_config.cc

@@ -426,6 +426,8 @@ void setupROMConfigOption(po::options_description &rom_cfg)
             "File name for libROM snapshot/POD matrices.")
         ("ROM.offline.save_librom_snapshot", po::value<bool>()->default_value(false),
             "Save libROM snapshot file at FOM simulation.")
+        ("ROM.offline.librom_snapshot_freq", po::value<int>()->default_value(-1),
+            "Frequency of saving libROM snapshot file at FOM simulation.")
         ("ROM.offline.variable", po::value<std::string>()->default_value(""),
             "FOM variable to perform POD: either orbitals or potential.")
         ("ROM.basis.number_of_potential_basis", po::value<int>()->default_value(-1),

src/rom_Control.h

@@ -46,6 +46,7 @@ struct ROMPrivateOptions
 
     /* save librom snapshot matrix at FOM simulation. */
     bool save_librom_snapshot = false;
+    int librom_snapshot_freq = -1;
 
     /* options for ROM building */
     int num_potbasis = -1;