From 0e417ef4f7fb6a785c90b52711bdc33dd08d80d8 Mon Sep 17 00:00:00 2001
From: Marcin Kirsz <mkirsz@ed.ac.uk>
Date: Wed, 19 Feb 2025 13:00:05 +0000
Subject: [PATCH] Dataset histogram tool
---
bin/tadah_cli.cpp | 246 +++++++++++++++++++++++++++++++++++-----------
bin/tadah_cli.h | 5 +
2 files changed, 191 insertions(+), 60 deletions(-)
diff --git a/bin/tadah_cli.cpp b/bin/tadah_cli.cpp
index 1fdd5e8..0cd6010 100644
--- a/bin/tadah_cli.cpp
+++ b/bin/tadah_cli.cpp
@@ -393,6 +393,19 @@ TadahCLI::TadahCLI():
->required()
->check(CLI::ExistingFile);
+ /*---------------------------------------------------------------------------*/
+ /* DB RESCALE */
+ /*---------------------------------------------------------------------------*/
+ usage =
+ "Add energy rescaling factors to dataset(s)\n";
+ rescale = db->add_subcommand("rescale", usage);
+
+ usage = "Specify one or more Tadah! datasets\n to add energy rescaling factors\n"
+ "The output is saved to new datasets(s) named:\n"
+ "ORIGNAL_FILE_rescaled\n";
+ rescale->add_option("-d,--datasets", datasets, usage)
+ ->required()
+ ->check(CLI::ExistingFile);
/*---------------------------------------------------------------------------*/
/* DESCRIPTORS */
@@ -511,12 +524,11 @@ TadahCLI::TadahCLI():
/*---------------------------------------------------------------------------*/
usage =
- "Plot basis functions\n(and optionally cutoff values)\nused in two- and many-body expansions.\n"
- "GNUPLOT plotting IS NOT IMPLEMENTED everything else should work\n";
+ "Plot basis functions\n(and optionally cutoff values)\nused in two- and many-body expansions.\n";
bf = plot->add_subcommand("bf", usage);
usage =
- "This function can generate a formatted text file for plotting with external software, or it can use gnuplot (if available during Tadah! compilation) for visualization.\n"
+ "This function can generate a formatted text file for plotting with external software.\n"
"Input must be either a trained potential model or a configuration file with the following keys:\n"
" - SGRID2B (or SGRIDMB) <--REQUIRED\n"
" - CGRID2B (or CGRIDMB) <--REQUIRED\n"
@@ -529,15 +541,21 @@ TadahCLI::TadahCLI():
bf->usage(usage);
usage =
- "Provide either a potential file\nor a config file containing\nthe necessary keys.\n";
+ "Provide either a potential file\nor a config file containing\nthe necessary keys.\n"
+ "The file must contain the following keys:\n"
+ " - INIT2B | INITMB\n"
+ " - TYPE2B | TYPEMB\n"
+ " - RCUT2B | RCUTMB\n"
+ " - RCTYPE2B | RCTYPEMB\n"
+ " - CGRID2B | CGRIDMB\n"
+ " - SGRID2B | SGRIDMB\n";
bf->add_option("-c,--config", config_file, usage)
->check(CLI::ExistingFile)
->required();
usage =
- "Specify the output file for text data\nand (optionally) a plot file using gnuplot.\n"
- "Supported plot file extensions:\n.png, .pdf, .eps, .svg.\n"
+ "Specify the output file for text data.\n"
"Pathnames must not exist.\n";
bf->add_option("-o,--outfile", out_files, usage)
@@ -547,15 +565,15 @@ TadahCLI::TadahCLI():
->required();
bf->add_option("-t,--type", types,
- "Specify the type of basis function and interaction:\n"
- " - \"B 2b Y/N\": Blips for two-body interactions\n"
- " - \"B mb Y/N\": Blips for many-body interactions\n"
- " - \"G 2b Y/N\": Gaussians for two-body interactions\n"
- " - \"G mb Y/N\": Gaussians for many-body interactions\n"
- "Y/N indicates whether to plot the cutoff function.\n")
+ "Specify whether to plot two- or many-body grid\n"
+ "Y/N indicates whether to also plot the cutoff function.\n"
+ " - \"2b Y/N\": Plot grid for TYPE2B\n"
+ " - \"mb Y/N\": Plot grid for TYPEMB\n"
+ "\n")
->required();
- bf->add_flag("-s,--scale", "Scale the heights of the basis\nfunctions by the cutoff value.\n");
+ bf->add_flag("-D,--Derivative", "Will plot derivatives of\nbasis functions and cutoffs.\n");
+ bf->add_flag("-s,--scale", "Rescale the heights of the basis\nfunctions by the cutoff value.\n");
usage =
"Indices of basis functions to be plotted\n"
@@ -581,8 +599,7 @@ TadahCLI::TadahCLI():
/*---------------------------------------------------------------------------*/
usage =
- "Plot two-body potential.\n"
- "GNUPLOT plotting IS NOT IMPLEMENTED everything else should work\n";
+ "Plot two-body potential.\n";
twobody = plot->add_subcommand("twobody", usage);
@@ -597,8 +614,7 @@ TadahCLI::TadahCLI():
->required();
usage =
- "Specify the output file for text data\nand (optionally) a plot file using gnuplot.\n"
- "Supported plot file extensions:\n.png, .pdf, .eps, .svg.\n"
+ "Specify the output file for text data.\n"
"Pathnames must not exist.\n";
twobody->add_option("-o,--outfile", out_files, usage)
@@ -627,8 +643,7 @@ TadahCLI::TadahCLI():
/*---------------------------------------------------------------------------*/
usage =
- "Plot cutoffs.\n"
- "GNUPLOT plotting IS NOT IMPLEMENTED everything else should work\n";
+ "Plot cutoffs.\n";
cutoff = plot->add_subcommand("cutoff", usage);
@@ -638,8 +653,7 @@ TadahCLI::TadahCLI():
cutoff->usage(usage);
usage =
- "Specify the output file for text data\nand (optionally) a plot file using gnuplot.\n"
- "Supported plot file extensions:\n.png, .pdf, .eps, .svg.\n"
+ "Specify the output file for text data.\n"
"Pathnames must not exist.\n";
cutoff->add_option("-o,--outfile", out_files, usage)
@@ -663,6 +677,39 @@ TadahCLI::TadahCLI():
cutoff->add_flag("-V,--Verbose", verbose,
"Enable verbose output for detailed information.\n");
+
+/*---------------------------------------------------------------------------*/
+/* PLOT DATA */
+/*---------------------------------------------------------------------------*/
+
+usage =
+ "Visualize Tadah! datasets.\n";
+
+vdata = plot->add_subcommand("vdata", usage);
+
+usage =
+ "This command provides tools for data visualization.\n"
+ "It generates a temperature vs. density histogram.\n"
+ "It counts the number of configurations that fall within each 2D bin (T, rho).\n"
+ "The formatted output is T rho count, where T and rho are the centers of the bins.\n";
+
+vdata->usage(usage);
+
+usage =
+ "One or more datasets for prediction.\n";
+
+vdata->add_option("-d,--datasets", datasets, usage)
+ ->required();
+
+vdata->add_option("-b,--bins", sizes, "Number of bins in the x and y directions.\n")
+ ->required();
+
+vdata->add_option("-n,--numeric", outprec,
+ "Set the number of decimal places for numerical output.\n");
+
+vdata->add_flag("-V,--verbose", verbose,
+ "Enable verbose output for detailed information.\n");
+
}
int TadahCLI::run(int argc, char** argv) {
@@ -699,6 +746,9 @@ int TadahCLI::run(int argc, char** argv) {
else if (*summary) {
return subsub_summary();
}
+ else if (*rescale) {
+ return subsub_rescale();
+ }
else if (*sample) {
return subsub_sample();
}
@@ -721,6 +771,9 @@ int TadahCLI::run(int argc, char** argv) {
else if (*cutoff) {
return subsub_cutoff();
}
+ else if (*vdata) {
+ return subsub_data();
+ }
}
return 0;
}
@@ -1182,6 +1235,21 @@ int TadahCLI::subsub_summary() {
}
return 0;
}
+int TadahCLI::subsub_rescale() {
+ if (rank!=0) return 0;
+ CLI::Timer timer_tot{"Rescaling", CLI::Timer::Big};
+ for (const auto &infile: datasets) {
+ StructureDB stdb;
+ stdb.add(infile);
+ for (auto &s: stdb) {
+ s.eweight = std::abs(1/s.energy);
+ }
+ std::string outfile = infile + "_rescaled";
+ stdb.dump_to_file(outfile);
+ }
+ if (verbose) std::cout << timer_tot.to_string() << std::endl;
+ return 0;
+}
int TadahCLI::subsub_sample() {
if (rank!=0) return 0;
@@ -1517,46 +1585,47 @@ int TadahCLI::subsub_bf() {
Config config(config_file);
DC_Selector DCS(config);
- v_type cgrid;
- v_type sgrid;
-
boost::to_upper(types[0]);
boost::to_upper(types[1]);
- boost::to_upper(types[2]);
Cut_Base *fcut = nullptr;
- if (types[1]=="2B") {
- DCS.d2b->get_grid(config, "CGRID2B", cgrid);
- DCS.d2b->get_grid(config, "SGRID2B", sgrid);
- if (types[2]=="Y") {
+ double (*fb)(double,double,double) = nullptr;
+ std::string cgridtype;
+ std::string sgridtype;
+ std::string dtype;
+ if (types[0]=="2B") {
+ cgridtype="CGRID2B";
+ sgridtype="SGRID2B";
+ dtype = config.get<std::string>("TYPE2B");
+ if (types[1]=="Y" || bf->count("--scale")) {
double rcut = config.get<double>("RCUT2BMAX");
fcut = CONFIG::factory<Cut_Base,double>( config.get<std::string>("RCTYPE2B"), rcut);
}
- }
- else if (types[1]=="MB") {
- DCS.dmb->get_grid(config, "CGRIDMB", cgrid);
- DCS.dmb->get_grid(config, "SGRIDMB", sgrid);
- if (types[2]=="Y") {
+ } else if (types[0]=="MB") {
+ cgridtype="CGRIDMB";
+ sgridtype="SGRIDMB";
+ dtype = config.get<std::string>("TYPEMB");
+ if (types[1]=="Y" || bf->count("--scale")) {
double rcut = config.get<double>("RCUTMBMAX");
fcut = CONFIG::factory<Cut_Base,double>( config.get<std::string>("RCTYPEMB"), rcut);
}
- }
- else {
+ } else {
throw std::runtime_error("Unsupported -t, --type: " + types[0] + " " + types[1]);
}
- double (*fb)(double,double,double) = nullptr;
- if (types[0]=="B") {
- std::cout << "B type: " << types[0] << std::endl;
- fb = &B;
- }
- else if (types[0]=="G") {
- std::cout << "G type: " << types[0] << std::endl;
- fb = &G;
- }
- else {
- throw std::runtime_error("Unsupported -t, --type: " + types[0] + " " + types[1]);
+ v_type cgrid;
+ v_type sgrid;
+ D_Base::get_grid(config, cgridtype, cgrid);
+ D_Base::get_grid(config, sgridtype, sgrid);
+
+ if (dtype == "D2_Blip" || dtype == "DM_Blip") {
+ if (bf->count("--Derivative")) { fb = &dB;} else { fb = &B; }
+ } else if (dtype == "D2_BP" || dtype == "DM_EAD" || dtype == "DM_mEAD") {
+ if (bf->count("--Derivative")) { fb = &dG;} else { fb = &G; }
+ } else {
+ throw std::runtime_error("Unsupported: " + dtype);
}
+
std::vector<size_t> idx;
if (bf->count("-i")) {
idx = parse_indices(indices);
@@ -1585,11 +1654,16 @@ int TadahCLI::subsub_bf() {
if (!bf->count("--numeric")) {
outprec = 5;
}
- bool scale = bf->count("--scale");
v_type cutoff_values (range.size(), 1.0);
- if (scale) {
- for (size_t i=0; i<range.size(); ++i) {
- cutoff_values[i] = fcut->calc(range[i]);
+ if (bf->count("--scale")) {
+ if(bf->count("--Derivative")) {
+ for (size_t i=0; i<range.size(); ++i) {
+ cutoff_values[i] = fcut->calc_prime(range[i]);
+ }
+ } else {
+ for (size_t i=0; i<range.size(); ++i) {
+ cutoff_values[i] = fcut->calc(range[i]);
+ }
}
}
@@ -1606,15 +1680,25 @@ int TadahCLI::subsub_bf() {
outfile << std::endl << std::endl;
}
- if (types[2]=="Y") {
- for (size_t i=0; i<range.size(); ++i) {
- outfile << std::fixed << std::setprecision(outprec)
- << std::setw(outprec+5)
- << range[i] << " "
- << std::setw(outprec+5) << fcut->calc(range[i]) << std::endl;
+ if (types[1]=="Y") {
+ if(bf->count("--Derivative")) {
+ for (size_t i=0; i<range.size(); ++i) {
+ outfile << std::fixed << std::setprecision(outprec)
+ << std::setw(outprec+5)
+ << range[i] << " "
+ << std::setw(outprec+5) << fcut->calc_prime(range[i]) << std::endl;
+ }
+ outfile << std::endl << std::endl;
+ }
+ else {
+ for (size_t i=0; i<range.size(); ++i) {
+ outfile << std::fixed << std::setprecision(outprec)
+ << std::setw(outprec+5)
+ << range[i] << " "
+ << std::setw(outprec+5) << fcut->calc(range[i]) << std::endl;
+ }
+ outfile << std::endl << std::endl;
}
- outfile << std::endl << std::endl;
-
}
outfile.flush();
@@ -1648,7 +1732,7 @@ int TadahCLI::subsub_twobody() {
size_t N = static_cast<size_t>(range[2]);
v_type range = linspace(start,stop,N);
- if (!bf->count("--numeric")) {
+ if (!twobody->count("--numeric")) {
outprec = 5;
}
@@ -1776,3 +1860,45 @@ int TadahCLI::subsub_cutoff() {
if (verbose) std::cout << timer_tot.to_string() << std::endl;
return 0;
}
+int TadahCLI::subsub_data() {
+ if (rank!=0) return 0;
+ CLI::Timer timer_tot{"Data Visualiser", CLI::Timer::Big};
+
+ if(vdata->count("--Verbose"))
+ set_verbose();
+
+ if (datasets.size()<1) throw std::runtime_error("At least one dataset is required. Check -d, --datasets");
+ if (sizes.size()!=2) throw std::runtime_error("Number of bins are requires. Provide two integer values. Check -b, --bins\n");
+ int x_bins = sizes[0];
+ int y_bins = sizes[1];
+
+ std::vector<std::pair<double,double>> data_2d;
+
+ std::vector<StructureDB> stdbs(datasets.size());
+ for (size_t i=0; i < stdbs.size(); ++i) {
+ stdbs[i].add(datasets[i]);
+ if (verbose) std::cout << datasets[i] << " " << stdbs[i].summary();
+ }
+
+ for (size_t i=0; i<stdbs.size(); ++i) {
+ for (size_t j=0; j<stdbs[i].size(); ++j) {
+ Structure &st = stdbs[i](j);
+ double T = st.get_temperature();
+ double rho = st.get_density();
+ data_2d.push_back(std::make_pair(T,rho));
+ }
+ }
+
+ std::vector<histogram_bin> histogram = generate_2d_histogram(data_2d, x_bins, y_bins);
+
+ for (const auto& bin : histogram) {
+ double x_center, y_center;
+ int count;
+ std::tie(x_center, y_center, count) = bin;
+ std::cout << x_center << " " << y_center << " " << count << "\n";
+ }
+
+ if (is_verbose()) std::cout << "Done!" << std::endl;
+ if (verbose) std::cout << timer_tot.to_string() << std::endl;
+ return 0;
+}
diff --git a/bin/tadah_cli.h b/bin/tadah_cli.h
index fd2b7fe..edb0513 100644
--- a/bin/tadah_cli.h
+++ b/bin/tadah_cli.h
@@ -61,11 +61,13 @@ private:
int subsub_join();
int subsub_split();
int subsub_summary();
+ int subsub_rescale();
int subsub_dcalc();
int sub_swriter();
int subsub_bf();
int subsub_twobody();
int subsub_cutoff();
+ int subsub_data();
int flag_version();
/* Return a vector of absolute paths to every file in a directory.
@@ -89,6 +91,7 @@ public:
CLI::App *split=nullptr;
CLI::Option_group *split_group=nullptr;
CLI::App *summary=nullptr;
+ CLI::App *rescale=nullptr;
CLI::App *desc=nullptr;
CLI::App *dcalc=nullptr;
CLI::App *swriter=nullptr;
@@ -96,6 +99,8 @@ public:
CLI::App *bf=nullptr;
CLI::App *cutoff=nullptr;
CLI::App *twobody=nullptr;
+ CLI::App *vdata=nullptr;
+ CLI::Option_group *data_group=nullptr;
};
#endif
--
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