TT-MetaD

.ci/install.itensor

@@ -0,0 +1,29 @@
+#! /usr/bin/env bash
+
+set -e
+set -x
+
+# Directory containing this script (i.e. .ci/)
+CI_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+
+# Install ITensor v3 dependencies
+sudo apt-get install -y libopenblas-dev libhdf5-dev
+
+ITENSOR_VERSION=3.2.0
+ITENSOR_INSTALL_DIR="$HOME/opt/itensor"
+
+cd "$(mktemp -dt plumed.XXXXXX)"
+
+wget https://github.com/ITensor/ITensor/archive/refs/tags/v${ITENSOR_VERSION}.tar.gz
+tar xzf v${ITENSOR_VERSION}.tar.gz
+cd ITensor-${ITENSOR_VERSION}
+
+# Use the CI-specific options.mk (OpenBLAS + system HDF5)
+cp "$CI_DIR/options.mk.itensor" options.mk
+
+make
+
+# Copy the built library and headers to the install directory
+mkdir -p "$ITENSOR_INSTALL_DIR"
+cp -r lib "$ITENSOR_INSTALL_DIR/"
+cp -r itensor "$ITENSOR_INSTALL_DIR/"

.ci/options.mk.itensor

@@ -0,0 +1,79 @@
+### CI-specific options.mk for ITensor v3
+### Uses OpenBLAS and system HDF5 (installed via apt on ubuntu-22.04).
+### Copy this file to the ITensor source directory as options.mk before building.
+
+## Compiler
+CCCOM=g++ -m64 -std=c++17 -fconcepts -fPIC
+
+## BLAS/LAPACK: use OpenBLAS (apt install libopenblas-dev)
+PLATFORM=lapack
+BLAS_LAPACK_LIBFLAGS=-lpthread -lopenblas
+
+## HDF5
+HDF5_CFLAGS  := $(shell pkg-config --cflags hdf5-serial 2>/dev/null || pkg-config --cflags hdf5 2>/dev/null)
+HDF5_LDFLAGS := $(shell pkg-config --libs-only-L hdf5-serial 2>/dev/null || pkg-config --libs-only-L hdf5 2>/dev/null)
+
+## OpenMP multithreading
+ITENSOR_USE_OMP=1
+
+## Optimization flags
+OPTIMIZATIONS=-O2 -DNDEBUG -Wall -Wno-unknown-pragmas
+
+## Debug flags
+DEBUGFLAGS=-DDEBUG -g -Wall -Wno-unknown-pragmas -pedantic
+
+## Do not build dynamic libraries (static linking is simpler in CI)
+ITENSOR_MAKE_DYLIB=0
+
+###
+### Remaining variables are derived; no need to modify below.
+###
+
+PREFIX=$(THIS_DIR)
+
+ITENSOR_LIBDIR=$(PREFIX)/lib
+ITENSOR_INCLUDEDIR=$(PREFIX)
+
+ITENSOR_LIBNAMES=itensor
+ITENSOR_LIBFLAGS=$(patsubst %,-l%, $(ITENSOR_LIBNAMES))
+ITENSOR_LIBFLAGS+= $(BLAS_LAPACK_LIBFLAGS)
+ITENSOR_LIBGFLAGS=$(patsubst %,-l%-g, $(ITENSOR_LIBNAMES))
+ITENSOR_LIBGFLAGS+= $(BLAS_LAPACK_LIBFLAGS)
+ITENSOR_LIBS=$(patsubst %,$(ITENSOR_LIBDIR)/lib%.a, $(ITENSOR_LIBNAMES))
+ITENSOR_GLIBS=$(patsubst %,$(ITENSOR_LIBDIR)/lib%-g.a, $(ITENSOR_LIBNAMES))
+
+ITENSOR_INCLUDEFLAGS=-I'$(ITENSOR_INCLUDEDIR)' $(BLAS_LAPACK_INCLUDEFLAGS)
+
+ifneq ($(strip $(HDF5_CFLAGS)),)
+ITENSOR_USE_HDF5 = 1
+# -DH5_USE_110_API: use HDF5 1.10-compatible API on HDF5 >= 1.12, which changed
+# H5Oget_info_by_name to a 5-argument form incompatible with ITensor's h5 utility code.
+ITENSOR_INCLUDEFLAGS += $(HDF5_CFLAGS) -DITENSOR_USE_HDF5 -DH5_USE_110_API
+ITENSOR_LIBFLAGS += $(HDF5_LDFLAGS) -lhdf5 -lhdf5_hl
+ITENSOR_LIBGFLAGS += $(HDF5_LDFLAGS) -lhdf5 -lhdf5_hl
+endif
+
+ifndef CCCOM
+$(error Makefile variable CCCOM not defined in options.mk; please define it.)
+endif
+
+ifdef ITENSOR_USE_OMP
+ITENSOR_INCLUDEFLAGS += -DITENSOR_USE_OMP -fopenmp
+ITENSOR_LIBFLAGS += -fopenmp
+ITENSOR_LIBGFLAGS += -fopenmp
+endif
+
+CCFLAGS=-I. $(ITENSOR_INCLUDEFLAGS) $(OPTIMIZATIONS) -Wno-unused-variable
+CCGFLAGS=-I. $(ITENSOR_INCLUDEFLAGS) $(DEBUGFLAGS)
+LIBFLAGS=-L'$(ITENSOR_LIBDIR)' $(ITENSOR_LIBFLAGS)
+LIBGFLAGS=-L'$(ITENSOR_LIBDIR)' $(ITENSOR_LIBGFLAGS)
+
+## Determine shared library extension
+UNAME_S := $(shell uname -s)
+ifeq ($(UNAME_S),Darwin)
+  DYLIB_EXT ?= dylib
+  DYLIB_FLAGS ?= -dynamiclib
+else
+  DYLIB_EXT ?= so
+  DYLIB_FLAGS ?= -shared
+endif

.github/workflows/linuxWF.yml

@@ -68,6 +68,23 @@ jobs:
 
         # the flags above enable the use of both libmetatomic and libtorch
         echo "PLUMED_CONFIG=$PLUMED_CONFIG --enable-libmetatomic --enable-libtorch" >> $GITHUB_ENV
+    - name: Install ITensor
+      if: ${{ contains( matrix.variant, '-mpi-' ) }}
+      run: |
+        .ci/install.itensor
+    - name: Configure ITensor
+      if: ${{ contains( matrix.variant, '-mpi-' ) }}
+      run: |
+        ITENSOR_DIR="$HOME/opt/itensor"
+        HDF5_CFLAGS=$(pkg-config --cflags hdf5-serial 2>/dev/null || pkg-config --cflags hdf5 2>/dev/null || echo "-I/usr/include/hdf5/serial")
+        HDF5_LIBDIR=$(pkg-config hdf5-serial --libs-only-L 2>/dev/null || pkg-config hdf5 --libs-only-L 2>/dev/null || echo "-L/usr/lib/x86_64-linux-gnu/hdf5/serial")
+        echo "LDFLAGS=$LDFLAGS -L${ITENSOR_DIR}/lib ${HDF5_LIBDIR}" >> $GITHUB_ENV
+        echo "CPPFLAGS=$CPPFLAGS -I${ITENSOR_DIR} ${HDF5_CFLAGS} -DITENSOR_USE_HDF5 -DITENSOR_USE_OMP -D__ITENSOR_LAPACK_WRAP_h -DH5_USE_110_API" >> $GITHUB_ENV
+        # temporary until configure.ac is updated to detect ITensor
+        echo "CXXFLAGS=-O3 -fconcepts" >> $GITHUB_ENV
+        echo "LIBS=-litensor -lopenblas -lhdf5 -lhdf5_hl" >> $GITHUB_ENV
+        # this will be uncommented after the configure.ac modifications
+        #echo "PLUMED_CONFIG=$PLUMED_CONFIG --enable-libitensor" >> $GITHUB_ENV
     - name: Install tools for setting up the manuals
       if: contains( matrix.variant, '-doc-' )
       run: |

.gitignore

@@ -27,4 +27,5 @@ makefile.dep
 __pycache__
 #to not export personal pyenv settings
 .python-version
-
+.vscode
+.claude

regtest/.gitignore

@@ -45,6 +45,7 @@
 !/wham
 !/metatomic
 !/sizeshape
+!/ttsketch
 !/xsprint
 
 # These files we just want to ignore completely

regtest/ttsketch/Makefile

@@ -0,0 +1 @@
+include ../scripts/module.make

regtest/ttsketch/rt-ttmetad/COLVAR.reference

@@ -0,0 +1,24 @@
+#! FIELDS time phi psi tt.bias
+#! SET min_phi -pi
+#! SET max_phi pi
+ 0.000000  -1.2379   1.9470   0.0000
+ 1.000000  -1.4839   1.9381   0.0000
+ 2.000000  -1.3243   1.9663   0.8644
+ 3.000000  -1.3340   1.9885   2.0694
+ 4.000000  -1.4613   1.8901   2.9094
+ 5.000000  -1.2202   2.0306   2.8990
+ 6.000000  -1.3883   1.8776   4.7976
+ 7.000000  -1.5481   1.9488   4.5938
+ 8.000000  -1.8429   1.9025   1.0045
+ 9.000000  -2.2424   1.9813   0.1537
+ 10.000000  -1.1482   1.9684   3.9692
+ 11.000000  -1.7580   1.9807   2.4606
+ 12.000000  -1.3186   1.9486   3.4383
+ 13.000000  -2.9911   1.9547  -0.1836
+ 14.000000  -1.4112   2.0415   4.1799
+ 15.000000  -2.5995   1.9166   0.7751
+ 16.000000  -1.4608   1.9433   5.2919
+ 17.000000  -1.3791   2.0625   6.2402
+ 18.000000  -1.6771   1.9433   5.3378
+ 19.000000  -1.5241   1.9642   7.8989
+ 20.000000  -1.1997   1.9296   6.6496

regtest/ttsketch/rt-ttmetad/HILLS.reference

@@ -0,0 +1,4 @@
+#! FIELDS time phi psi sigma_phi sigma_psi height biasf
+#! SET min_phi -pi
+#! SET max_phi pi
+   20.000000   -1.199652    1.929639    0.200000    0.200000    1.200000   -1.000000

regtest/ttsketch/rt-ttmetad/Makefile

@@ -0,0 +1 @@
+include ../../scripts/test.make

regtest/ttsketch/rt-ttmetad/config

@@ -0,0 +1,3 @@
+plumed_modules=ttsketch
+type=driver
+arg="--plumed plumed.dat --trajectory-stride 500 --timestep 0.002 --igro traj.gro"

regtest/ttsketch/rt-ttmetad/plumed.dat

@@ -0,0 +1,22 @@
+phi:   TORSION ATOMS=5,7,9,15 NOPBC
+psi:   ANGLE   ATOMS=7,9,15
+
+tt: TTMETAD ...
+  ARG=phi,psi
+  SIGMA=0.20,0.20
+  HEIGHT=1.20
+  PACE=500
+  TEMP=300.0
+  FILE=HILLS
+  FMT=%12.6f
+  SKETCH_RANK=2
+  SKETCH_INITRANK=4
+  SKETCH_PACE=5000
+  INTERVAL_MIN=-3.14159,0.0
+  INTERVAL_MAX=3.14159,3.14159
+  SKETCH_NBASIS=5
+  SKETCH_ALPHA=1.0
+  DETERMINISTIC
+...
+
+PRINT STRIDE=500 FILE=COLVAR ARG=phi,psi,tt.bias FMT=%8.4f