*******> update.3 Author: Vinicius Cruzeiro Date: August 7, 2022 Programs: sander, tcpb-cpp Description: This fixes bugs related to TCPB-cpp and updates it to the latest version. -------------------------------------------------------------------------------- AmberTools/src/sander/qm2_extern_tc_module.F90 | 7 +- AmberTools/src/sander/qm_mm.F90 | 2 +- AmberTools/src/sander/remd.F90 | 2 +- AmberTools/src/sander/tcpb_module.F90 | 47 +- AmberTools/src/tcpb-cpp/CMakeLists.txt | 7 - AmberTools/src/tcpb-cpp/Makefile | 34 +- AmberTools/src/tcpb-cpp/README.md | 62 +- .../src/tcpb-cpp/api_examples/CMakeLists.txt | 20 - AmberTools/src/tcpb-cpp/api_examples/cpp/Makefile | 13 - .../src/tcpb-cpp/api_examples/cpp/reference.log | 98 - .../src/tcpb-cpp/api_examples/cpp/terachem.inp | 9 - .../src/tcpb-cpp/api_examples/cpp/test_api.cpp | 321 --- .../src/tcpb-cpp/api_examples/fortran/Makefile | 13 - .../tcpb-cpp/api_examples/fortran/reference.log | 98 - .../src/tcpb-cpp/api_examples/fortran/terachem.inp | 9 - .../src/tcpb-cpp/api_examples/fortran/test_api.F90 | 316 --- .../src/tcpb-cpp/api_examples/python/reference.log | 98 - .../src/tcpb-cpp/api_examples/python/terachem.inp | 9 - .../src/tcpb-cpp/api_examples/python/test_api.py | 259 -- AmberTools/src/tcpb-cpp/configure | 7 +- AmberTools/src/tcpb-cpp/docs/Doxyfile | 2537 -------------------- AmberTools/src/tcpb-cpp/examples/CMakeLists.txt | 4 +- .../src/tcpb-cpp/examples/api/CMakeLists.txt | 39 + AmberTools/src/tcpb-cpp/examples/api/cpp/Makefile | 13 + .../src/tcpb-cpp/examples/api/cpp/reference.log | 131 + .../src/tcpb-cpp/examples/api/cpp/terachem.inp | 7 + .../src/tcpb-cpp/examples/api/cpp/test_api.cpp | 426 ++++ .../examples/api/cpp_openmm/2waters.prmtop | 138 ++ .../examples/api/cpp_openmm/2waters.qmregion | 6 + .../src/tcpb-cpp/examples/api/cpp_openmm/Makefile | 13 + .../tcpb-cpp/examples/api/cpp_openmm/reference.log | 35 + .../tcpb-cpp/examples/api/cpp_openmm/terachem.inp | 10 + .../tcpb-cpp/examples/api/cpp_openmm/test_api.cpp | 193 ++ .../src/tcpb-cpp/examples/api/fortran/Makefile | 13 + .../tcpb-cpp/examples/api/fortran/reference.log | 133 + .../src/tcpb-cpp/examples/api/fortran/terachem.inp | 7 + .../src/tcpb-cpp/examples/api/fortran/test_api.F90 | 417 ++++ .../examples/api/fortran_openmm/2waters.prmtop | 138 ++ .../examples/api/fortran_openmm/2waters.qmregion | 6 + .../tcpb-cpp/examples/api/fortran_openmm/Makefile | 13 + .../examples/api/fortran_openmm/reference.log | 38 + .../examples/api/fortran_openmm/terachem.inp | 10 + .../examples/api/fortran_openmm/test_api.F90 | 194 ++ .../src/tcpb-cpp/examples/api/python/reference.log | 131 + .../src/tcpb-cpp/examples/api/python/terachem.inp | 7 + .../src/tcpb-cpp/examples/api/python/test_api.py | 348 +++ .../examples/api/python_openmm/2waters.prmtop | 138 ++ .../examples/api/python_openmm/2waters.qmregion | 6 + .../examples/api/python_openmm/reference.log | 35 + .../examples/api/python_openmm/terachem.inp | 10 + .../examples/api/python_openmm/test_api.py | 154 ++ AmberTools/src/tcpb-cpp/pytcpb/CMakeLists.txt | 5 +- AmberTools/src/tcpb-cpp/pytcpb/pytcpb/__init__.py | 25 +- AmberTools/src/tcpb-cpp/pytcpb/setup.py | 88 +- AmberTools/src/tcpb-cpp/src/api.cpp | 107 +- AmberTools/src/tcpb-cpp/src/api.h | 11 +- AmberTools/src/tcpb-cpp/src/input.cpp | 14 +- AmberTools/src/tcpb-cpp/src/output.cpp | 6 + AmberTools/src/tcpb-cpp/src/output.h | 7 + AmberTools/src/tcpb-cpp/src/tcpbfiles | 1 - AmberTools/src/tcpb-cpp/tests/CMakeLists.txt | 14 - AmberTools/src/tcpb-cpp/tests/input/tc.bohr | 10 - AmberTools/src/tcpb-cpp/tests/input/tc.broken | 9 - AmberTools/src/tcpb-cpp/tests/input/tc.method | 12 - AmberTools/src/tcpb-cpp/tests/input/tc.template | 12 - AmberTools/src/tcpb-cpp/tests/input/water.au | 5 - AmberTools/src/tcpb-cpp/tests/input/water.xyz | 5 - AmberTools/src/tcpb-cpp/tests/input_test.cpp | 192 -- AmberTools/src/tcpb-cpp/tests/socket_test.cpp | 145 -- .../tcpb-cpp/tests/tcpb-client-docker/Dockerfile | 54 - AmberTools/src/tcpb-cpp/tests/tcpb_test.cpp | 122 - 71 files changed, 3144 insertions(+), 4481 deletions(-) diff --git AmberTools/src/sander/qm2_extern_tc_module.F90 AmberTools/src/sander/qm2_extern_tc_module.F90 index 0ef1ea1..c045cab 100644 --- AmberTools/src/sander/qm2_extern_tc_module.F90 +++ AmberTools/src/sander/qm2_extern_tc_module.F90 @@ -133,7 +133,7 @@ contains call system('rm -f '//inpfile) call write_inpfile( trim(inpfile), trim(crdfile), trim(ptcfile), trim(tplfile), & nqmatoms, qmcoords, qmtypes, nclatoms, clcoords, & - tc_nml, do_grad, charge, spinmult ) + tc_nml, do_grad, charge, spinmult, nstep ) call_buffer='' subdir='' @@ -400,7 +400,7 @@ contains ! --------------------------------- subroutine write_inpfile( inpfile, crdfile, ptcfile, tplfile, & nqmatoms, qmcoords, qmtypes, nclatoms, clcoords, & - tc_nml, do_grad, charge, spinmult ) + tc_nml, do_grad, charge, spinmult, nstep ) use ElementOrbitalIndex, only : elementSymbol use qm2_extern_util_module, only: write_chgfile @@ -415,6 +415,7 @@ contains _REAL_ , intent(in) :: qmcoords(:,:) integer , intent(in) :: qmtypes(:) integer , intent(in) :: nclatoms + integer , intent(in) :: nstep _REAL_ , intent(in) :: clcoords(:,:) type(tc_nml_type) , intent(in) :: tc_nml logical, intent(in) :: do_grad @@ -469,7 +470,7 @@ contains write(iurun, '(2a)') 'scrdir ', tc_nml%scrdir write(iurun, '(2a)') 'keep_scr ', tc_nml%keep_scr - if ( .not. first_call ) then + if ( .not. first_call .and. nstep>0) then write(iurun, '(2a)') 'guess ', tc_nml%guess end if diff --git AmberTools/src/sander/qm_mm.F90 AmberTools/src/sander/qm_mm.F90 index d1f88ae..3170ec9 100644 --- AmberTools/src/sander/qm_mm.F90 +++ AmberTools/src/sander/qm_mm.F90 @@ -458,7 +458,7 @@ subroutine qm_mm(coords, natom, scaled_mm_charges, f, escf, periodic, & nclatoms, qmmm_struct%qm_xcrd, escf, & qmmm_struct%dxyzqm, qmmm_struct%dxyzcl) else if (qmmm_nml%qmtheory%ISTCPB) then - call get_tcpb_qmmm_forces(qmmm_struct%nquant_nlink, & + call get_tcpb_qmmm_forces(nstep, qmmm_struct%nquant_nlink, & qmmm_struct%qm_coords, & qmmm_struct%iqm_atomic_numbers, & nclatoms, qmmm_struct%qm_xcrd, escf, & diff --git AmberTools/src/sander/remd.F90 AmberTools/src/sander/remd.F90 index 15597da..0e2484c 100644 --- AmberTools/src/sander/remd.F90 +++ AmberTools/src/sander/remd.F90 @@ -3205,7 +3205,7 @@ subroutine hremd_exchange(rem_dim, x, ix, ih, ipairs, qsetup, do_list_update) !write(6,'(a,3f8.3)') 'DBG: New box: ', box(1:3) ! Call force on temporary coordinate array to get new energy call force(x, ix, ih, ipairs, xtemp, ftemp, expe, expe%vir, x(l96), & - x(l97), x(l98), x(l99), qsetup, do_list_update) + x(l97), x(l98), x(l99), qsetup, do_list_update,-1) ! ======================================================= ! Step 3: calculate free energy difference, delta diff --git AmberTools/src/sander/tcpb_module.F90 AmberTools/src/sander/tcpb_module.F90 index 9f00c5b..8e00dae 100644 --- AmberTools/src/sander/tcpb_module.F90 +++ AmberTools/src/sander/tcpb_module.F90 @@ -35,6 +35,7 @@ module tcpb_module integer :: dftgrid integer :: cisnumstates integer :: cistarget + logical :: recycleinitguess ! Controls if we will try to use the wavefunction from previous step logical :: debug ! print debug output end type tcpb_nml_type @@ -44,7 +45,7 @@ module tcpb_module contains ! Calculate the TCPB qmmm forces and energy - subroutine get_tcpb_qmmm_forces(nqmatoms, qmcoords, qmtypes, & + subroutine get_tcpb_qmmm_forces(nstep, nqmatoms, qmcoords, qmtypes, & & nclatoms, clcoords, escf, dxyzqm, dxyzcl, id) use ElementOrbitalIndex, only : elementSymbol @@ -63,13 +64,14 @@ contains _REAL_, intent(out) :: dxyzqm(3,nqmatoms) _REAL_, intent(out) :: dxyzcl(3,nclatoms) character(len=3), intent(in) :: id + integer, intent(in) :: nstep ! local variables _REAL_ :: tcpb_qmcoords(3*nqmatoms) character(len=5) :: qmatelsymb(nqmatoms) _REAL_ :: tcpb_mmcoords(3*nclatoms), tcpb_mmcharges(nclatoms) _REAL_ :: tcpb_dxyzqm(3*nqmatoms), tcpb_dxyzcl(3*nclatoms) - integer :: i, ierr + integer :: i, ierr, globaltreatment logical, save :: first_call = .true. ! Initialize output values as zero @@ -124,9 +126,16 @@ contains do i = 1, nqmatoms qmatelsymb(i) = trim(elementSymbol(qmtypes(i)))//CHAR(0) end do + ! globaltreatment handles how the initial guess for the wavefunction will be constructed + ! globaltreatment = 1 means that a new condition will be done from scratch + if (nstep<1 .or. .not. tcpb_nml%recycleinitguess) then + globaltreatment = 1 + else + globaltreatment = 0 + end if ! Compute energy and gradients with TCPB call tc_compute_energy_gradient(qmatelsymb,tcpb_qmcoords,nqmatoms,escf,tcpb_dxyzqm,tcpb_mmcoords,& - tcpb_mmcharges,nclatoms,tcpb_dxyzcl,0,ierr) + tcpb_mmcharges,nclatoms,tcpb_dxyzcl,globaltreatment,ierr) if (ierr == 0 .and. tcpb_nml%debug) then write(6,*) ">>> Computed energy and gradients with success with tc_compute_energy_gradient." write(6,*) @@ -202,6 +211,7 @@ contains character(len=3), intent(in) :: id character(len=5) :: qmatelsymb(nqmatoms) integer :: ierr, i + logical :: exstfl character(len=256) :: tcfile integer, parameter :: iurun = 10 @@ -240,8 +250,8 @@ contains write(6, '(2a)') '| Writing TeraChem input file to ', trim(tcfile) open(iurun, file=tcfile, iostat=ierr) if ( ierr > 0 ) then - call sander_bomb('tcpb_input_setting (tcpb_module)', & - 'Error opening TeraChem input file '//tcfile//' for writing', & + call sander_bomb('tcpb_input_setting', & + 'Error opening TeraChem input file '//trim(tcfile)//' for writing', & 'Will quit now') end if write(iurun, '(a,/,a)')'# Run using SANDER TCPB interface for TeraChem','#' @@ -261,8 +271,15 @@ contains write(iurun, '(a,i3)') 'charge ', qmmm_nml%qmcharge write(iurun, '(a,i3)') 'spinmult ', qmmm_nml%spin flush(iurun) + close(iurun) else tcfile = tcpb_nml%tcfile + inquire(file=tcfile, exist=exstfl) + if (.not. exstfl) then + call sander_bomb('tcpb_input_setting', & + 'TeraChem input file '//trim(tcfile)//' does not exist!', & + 'Will quit now.') + end if write(6, '(2a)') '| Reading TeraChem input file from ', trim(tcfile) end if @@ -329,17 +346,18 @@ contains integer :: dftgrid integer :: cisnumstates integer :: cistarget + integer :: recycleinitguess integer :: debug ! print debug output namelist /tc/ tcfile, host, port, method, basis, precision, dftd, cis, threall,& - convthre, maxit, dftgrid, cisnumstates, cistarget, debug + convthre, maxit, dftgrid, cisnumstates, cistarget, recycleinitguess, debug ! Default namelist variable values tcfile = '' host = '' port = -1 - basis = '6-31g' - method = 'blyp' + basis = '' + method = '' dftd = 'no' precision = 'mixed' cis = 'no' @@ -348,7 +366,8 @@ contains maxit = 100 dftgrid = 1 cisnumstates = 1 - cistarget = 1 + cistarget = 0 + recycleinitguess= 1 ! Controls if we will try to use the wavefunction from previous step debug = 0 ! Read namelist @@ -381,6 +400,15 @@ contains tcpb_nml%dftgrid = dftgrid tcpb_nml%cisnumstates = cisnumstates tcpb_nml%cistarget = cistarget + if ( recycleinitguess == 0) then + tcpb_nml%recycleinitguess = .false. + else if ( recycleinitguess > 0) then + tcpb_nml%recycleinitguess = .true. + else + call sander_bomb('read_tcpb_nml', & + '&tc recycleinitguess read error', & + 'Please check your input.') + end if if ( debug == 0) then tcpb_nml%debug = .false. else if ( debug > 0) then @@ -420,6 +448,7 @@ contains write(6,'(a,a)') ' cis : ', trim(self%cis) write(6,'(a,i0)') ' cisnumstates : ', self%cisnumstates write(6,'(a,i0)') ' cistarget : ', self%cistarget + write(6,'(a,l)') ' recycleinitguess : ', self%recycleinitguess write(6,'(a,l)') ' debug : ', self%debug end subroutine print_tcpb_nml diff --git AmberTools/src/tcpb-cpp/CMakeLists.txt AmberTools/src/tcpb-cpp/CMakeLists.txt index 62d0b6a..c454828 100644 --- AmberTools/src/tcpb-cpp/CMakeLists.txt +++ AmberTools/src/tcpb-cpp/CMakeLists.txt @@ -38,8 +38,6 @@ if(NOT INSIDE_AMBER) # build options option(INSTALL_HEADERS "Copy headers to the include/tcpb folder of the install directory." TRUE) - option(INSTALL_TESTS "Compile tests in the tests folder of the install directory" TRUE) - option(INSTALL_EXAMPLES "Compile examples in the exemples folder of the install directory" TRUE) option(BUILD_PYTHON "Install pytcpb in the Python environment" TRUE) @@ -58,7 +56,6 @@ if(NOT INSIDE_AMBER) endif() else() set(INSTALL_HEADERS TRUE) - set(INSTALL_TESTS FALSE) set(INSTALL_EXAMPLES FALSE) endif() @@ -76,12 +73,8 @@ if (BUILD_PYTHON AND NOT INSIDE_AMBER) endif() add_subdirectory(pytcpb) endif() -if (INSTALL_TESTS) - add_subdirectory(tests) -endif() if (INSTALL_EXAMPLES) add_subdirectory(examples) - add_subdirectory(api_examples) endif() #-------------------------------------------------------------- diff --git AmberTools/src/tcpb-cpp/Makefile AmberTools/src/tcpb-cpp/Makefile index 08e0b43..0dd1383 100644 --- AmberTools/src/tcpb-cpp/Makefile +++ AmberTools/src/tcpb-cpp/Makefile @@ -1,13 +1,12 @@ include config.h .NOTPARALLEL:clean install all -.PHONY: test +.PHONY: test pytcpb LIBSRC := src/exceptions.cpp \ src/client.cpp \ src/input.cpp \ src/output.cpp \ - src/server.cpp \ src/socket.cpp \ src/terachem_server.pb.cpp \ src/utils.cpp \ @@ -17,12 +16,6 @@ LIBOBJS := $(patsubst src/%.cpp, src/%.o, $(LIBSRC)) LIBNAME = libtcpb -TESTSRC := tests/input_test.cpp \ - tests/socket_test.cpp \ - tests/tcpb_test.cpp - -TESTBIN := $(patsubst tests/%.cpp, tests/%, $(TESTSRC)) - all: src/terachem_server.pb.cpp $(LIBNAME).so $(LIBNAME).so: $(LIBOBJS) @@ -60,26 +53,11 @@ clean: example: @cd examples/qm && make @cd examples/qmmm && make + @cd examples/api/fortran && make + @cd examples/api/fortran_openmm && make + @cd examples/api/cpp && make + @cd examples/api/cpp_openmm && make pytcpb: + @echo "[pyTCPB] Installing pyTCPB" @cd pytcpb && python setup.py install - -api_example: - @cd api_examples/fortran && make - @cd api_examples/cpp && make - -ifdef TESTDIR -test: $(TESTBIN) $(LIBDIR)/$(LIBNAME).so - @echo "TCPB: Running input_test" - @cd tests && ./input_test - @echo "TCPB: Running socket_test" - @cd tests && ./socket_test - @echo "TCPB: Running tcpb_test" - @cd tests && ./tcpb_test - -test-clean: - /bin/rm -f $(TESTBIN) - -tests/%: tests/%.cpp - $(CXX) $(TCPB_CXXFLAGS) -o $@ $< $(TESTS_LDFLAGS) -I$(INCDIR) -L$(LIBDIR) -endif diff --git AmberTools/src/tcpb-cpp/README.md AmberTools/src/tcpb-cpp/README.md index 21c29cf..1b86b69 100644 --- AmberTools/src/tcpb-cpp/README.md +++ AmberTools/src/tcpb-cpp/README.md @@ -2,47 +2,68 @@ This repository is designed to facilitate the communication between TeraChem and third party software. -The client and server (set by the TeraChem executable) use C-style sockets for communication, and Protocol Buffers for a clean, well-defined way to serialize TeraChem input & output. +The client and the server (set by the TeraChem executable) use C-style sockets for communication, and Protocol Buffers for a clean, well-defined way to serialize TeraChem input & output data. ## Requirements * Protocol Buffers >= 3.2.0 (`protoc` and `libprotobuf.so` for C++) +## Cloning this repo and setting up its submodules + +``` +git clone git@github.com:mtzgroup/tcpb-cpp.git tcpb-cpp +cd tcpb-cpp +git submodule init +git submodule update +``` + +## Obtaining and installing Protocol Buffers + +* Please refer to [this page](https://developers.google.com/protocol-buffers) for instructions on how to download and install Google’s Protocol Buffers libraries and executables. + +* At the time of writing, protocol buffers can be downloaded from (e.g., `protobuf-cpp-3.20.1.zip`) and installation instructions for C++ are provided at . + ## Installation (with configure script) -* Ensure `protoc` and `libprotobuf.so` are in your `PATH` and `LD_LIBRARY_PATH`, respectively +* Ensure `protoc` and `libprotobuf.so` (from Protocol Buffers) are in your `PATH` and `LD_LIBRARY_PATH`, respectively -* Run `./configure gnu`. Other compiler options are intel and clang (not tested). To pick another install location, like /usr/local, run `./configure --prefix=/usr/local gnu` +* Run `./configure gnu` if using GNU compilers or `./configure intel` if using Intel compilers. Other compiler options are intel and clang (not tested). To pick another install location, like /usr/local, run `./configure --prefix=/usr/local gnu` * Run `make install` -* To install the Python interface `pytcpb`, run `make pytcpb`. After installation, the API functions can be called from your custom Python script. Refer to `api_examples/python` for usage example. +* To install the Python interface *PyTCPB*, run `make pytcpb`. After installation, the API functions can be called from your custom Python script. Refer to `examples/api/python` for usage example. * Add the absolute path to `lib` into `LD_LIBRARY_PATH` ## Installation (with CMake) -* Ensure you have CMake version 3.8.0 or higher +* Ensure you have CMake version 3.8.0 or higher. * Run `mkdir build && cd build` -* To install, for example, with GNU compilers at /usr/local, run `cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local -DCOMPILER=GNU` +* To install, for example, with GNU compilers at /usr/local, run `cmake .. -DCMAKE_INSTALL_PREFIX=/usr/local -DCOMPILER=GNU`. To use Intel compilers, the option `-DCOMPILER=INTEL` must be specified instead. * Run `make install` -* The Python interface `pytcpb` is installed by default. To deactivate its installation, add `-DBUILD_PYTHON=FALSE` into your cmake command. After installation, the API functions can be called from your custom Python script. Refer to `api_examples/python` for usage example. +* The Python interface *PyTCPB* is installed by default. To deactivate its installation, add `-DBUILD_PYTHON=FALSE` into your CMake command. After installation, the API functions can be called from your custom Python script. Refer to `examples/api/python` for usage example. * Add the absolute path to `../lib` into `LD_LIBRARY_PATH` -## Tests +## Running TeraChem in server mode + +TeraChem needs to be active in server mode so that TCPB-cpp can connect to it. -* After installation with configure script, run `make test`. With CMake, the tests are automatically compiled and placed at the folder `tests` +TeraChem can be executed in server mode with the following command: +``` +terachem -s 12345 +``` +where `-s` specifies the port number to be used and 12345 is a value picked for illustration purposes only. By default, TeraChem will use all GPUs in the machine, but users can control which GPUs are accessible by using the `-g` in the TeraChem command above or by setting the `CUDA_VISIBLE_DEVICES` environment variable before running the command above. ## Examples -* Native examples: after installation with configure script, run `make example`. With CMake, the examples are automatically compiled and placed at the corresponding folder inside the folder `examples` +* **Using TCPB-cpp from different programming languages:** examples available at the folder `examples/api`. -* Examples using the API from different programming languages: after installation with configure script, run `make api_example`. With CMake, the API examples are automatically compiled and placed at the corresponding folder inside the folder `api_examples`. Currently, there are examples for Fortran, C++ and Python. +* **Native C++ examples:** after installation with configure script, run `make example`. With CMake, the examples are automatically compiled and placed at the corresponding folder inside the folder `examples` ## Notes for TeraChem Developers @@ -55,22 +76,7 @@ Also, it is critically important that the current values of MessageType enum are not changed since this is a key part of the protocol's header, determining how the server/client deserialize the incoming message. -### Branches and tests for any new features - -Extensions of the protocol are encouraged, but please follow some basic guidelines: - -* Develop any new features in a branch to avoid accidentally pushing broken protocols to `master` - -* Add test cases for your protocol/job type - -* Use the BitBucket Pipelines Docker container to ensure your tests will pass when pushed - -* Submit a pull request for your branch to facilitate code review - -The `run_pipelines_tests.sh` script automates build, install, and testing for the repo. -The `run_docker_tests.sh` script wraps the magic Docker lines to do this with the container that Pipelines will use. - ## Contact -* Stefan Seritan -* Vinicius Wilian D. Cruzeiro \ No newline at end of file +* Vinicius Wilian D. Cruzeiro: +* Henry Wang: diff --git AmberTools/src/tcpb-cpp/api_examples/CMakeLists.txt AmberTools/src/tcpb-cpp/api_examples/CMakeLists.txt deleted file mode 100644 index 48c5b89..0000000 --- AmberTools/src/tcpb-cpp/api_examples/CMakeLists.txt +++ /dev/null @@ -1,20 +0,0 @@ -# executables - -add_executable(test_api_fortran fortran/test_api.F90) -target_link_libraries(test_api_fortran PUBLIC libtcpb PRIVATE protobuf::libprotobuf Threads::Threads) -install(TARGETS test_api_fortran DESTINATION ${CMAKE_INSTALL_PREFIX}/api_examples/fortran) -install(FILES ${tcpb_SOURCE_DIR}/api_examples/fortran/terachem.inp - ${tcpb_SOURCE_DIR}/api_examples/fortran/reference.log - DESTINATION ${CMAKE_INSTALL_PREFIX}/api_examples/fortran) - -add_executable(test_api_cpp cpp/test_api.cpp) -target_link_libraries(test_api_cpp PUBLIC libtcpb PRIVATE protobuf::libprotobuf Threads::Threads) -install(TARGETS test_api_cpp DESTINATION ${CMAKE_INSTALL_PREFIX}/api_examples/cpp) -install(FILES ${tcpb_SOURCE_DIR}/api_examples/cpp/terachem.inp - ${tcpb_SOURCE_DIR}/api_examples/cpp/reference.log - DESTINATION ${CMAKE_INSTALL_PREFIX}/api_examples/cpp) - -install(FILES ${tcpb_SOURCE_DIR}/api_examples/python/terachem.inp - ${tcpb_SOURCE_DIR}/api_examples/python/reference.log - ${tcpb_SOURCE_DIR}/api_examples/python/test_api.py - DESTINATION ${CMAKE_INSTALL_PREFIX}/api_examples/python) \ No newline at end of file diff --git AmberTools/src/tcpb-cpp/api_examples/cpp/Makefile AmberTools/src/tcpb-cpp/api_examples/cpp/Makefile deleted file mode 100644 index 0c5c290..0000000 --- AmberTools/src/tcpb-cpp/api_examples/cpp/Makefile +++ /dev/null @@ -1,13 +0,0 @@ -# This Makefile assumes you have installed the C++ TCPB client with make install -# and added the lib and include folders to your environment - -include ../../config.h - -LIBS=-L$(LIBDIR) -lprotobuf -ltcpb - -test_api_cpp: test_api.cpp - $(CXX) $(TCPB_CXXFLAGS) -o $@ $< -I$(INCDIR) $(LIBS) - -.PHONY: clean -clean: - @rm -v test_api_cpp diff --git AmberTools/src/tcpb-cpp/api_examples/cpp/reference.log AmberTools/src/tcpb-cpp/api_examples/cpp/reference.log deleted file mode 100644 index eaea166..0000000 --- AmberTools/src/tcpb-cpp/api_examples/cpp/reference.log +++ /dev/null @@ -1,98 +0,0 @@ - Attempting to connect to TeraChem server using host localhost and port 12345. - Successfully connected to TeraChem server. - TeraChem setup completed with success. - - Computed energy and gradient with success. - Results from 1st calculation (only one water molecule in the QM region) -E = -76.0022844544 Hartrees -QM Grad( 1,:) = -0.0642463980 0.0371034421 -0.0713540769 Hartree/Bohr -QM Grad( 2,:) = -0.0266141637 -0.0518086391 0.0036397418 Hartree/Bohr -QM Grad( 3,:) = 0.0908605618 0.0147051970 0.0677143350 Hartree/Bohr - - Computed energy and gradient with success. - Results from 2nd calculation (one water molecule in the QM region and five in the MM region) -E = -76.0387136201 Hartrees -QM Grad( 1,:) = -0.0620229271 0.0306042943 -0.0738584016 Hartree/Bohr -QM Grad( 2,:) = -0.0247730873 -0.0505936308 0.0075343381 Hartree/Bohr -QM Grad( 3,:) = 0.0745816528 0.0010694430 0.0466698947 Hartree/Bohr -MM Grad( 1,:) = 0.0168460146 0.0176625994 0.0202798048 Hartree/Bohr -MM Grad( 2,:) = -0.0052857623 -0.0011172724 -0.0025479307 Hartree/Bohr -MM Grad( 3,:) = -0.0012305920 -0.0049104978 -0.0011060955 Hartree/Bohr -MM Grad( 4,:) = 0.0047910607 -0.0062894775 -0.0061427873 Hartree/Bohr -MM Grad( 5,:) = -0.0070490574 0.0137660690 0.0088585533 Hartree/Bohr -MM Grad( 6,:) = 0.0004543010 0.0013874752 0.0023238939 Hartree/Bohr -MM Grad( 7,:) = 0.0018573907 0.0001200172 -0.0051518439 Hartree/Bohr -MM Grad( 8,:) = -0.0002598900 -0.0006551838 0.0015615262 Hartree/Bohr -MM Grad( 9,:) = -0.0003799401 0.0007765589 0.0013011774 Hartree/Bohr -MM Grad( 10,:) = -0.0046678908 0.0008143731 0.0014719501 Hartree/Bohr -MM Grad( 11,:) = 0.0058564215 -0.0020721506 -0.0012500193 Hartree/Bohr -MM Grad( 12,:) = 0.0011666958 -0.0005276604 0.0001503221 Hartree/Bohr -MM Grad( 13,:) = -0.0018475363 -0.0000440524 0.0030407459 Hartree/Bohr -MM Grad( 14,:) = 0.0003060683 0.0010221057 -0.0022137623 Hartree/Bohr -MM Grad( 15,:) = 0.0016570779 -0.0010130103 -0.0009213657 Hartree/Bohr - - Computed energy and gradient with success. - Results from 3rd calculation (just repeating the 2nd calculation) -E = -76.0387136124 Hartrees -QM Grad( 1,:) = -0.0620194224 0.0305990472 -0.0738538336 Hartree/Bohr -QM Grad( 2,:) = -0.0247672481 -0.0505865888 0.0075303582 Hartree/Bohr -QM Grad( 3,:) = 0.0745721809 0.0010677291 0.0466694660 Hartree/Bohr -MM Grad( 1,:) = 0.0168462242 0.0176626629 0.0202796602 Hartree/Bohr -MM Grad( 2,:) = -0.0052857901 -0.0011172756 -0.0025478975 Hartree/Bohr -MM Grad( 3,:) = -0.0012306275 -0.0049105037 -0.0011060668 Hartree/Bohr -MM Grad( 4,:) = 0.0047909573 -0.0062894161 -0.0061427556 Hartree/Bohr -MM Grad( 5,:) = -0.0070489469 0.0137659194 0.0088585058 Hartree/Bohr -MM Grad( 6,:) = 0.0004543197 0.0013874419 0.0023238764 Hartree/Bohr -MM Grad( 7,:) = 0.0018573313 0.0001199891 -0.0051518122 Hartree/Bohr -MM Grad( 8,:) = -0.0002598724 -0.0006551795 0.0015615109 Hartree/Bohr -MM Grad( 9,:) = -0.0003799223 0.0007765528 0.0013011662 Hartree/Bohr -MM Grad( 10,:) = -0.0046678654 0.0008143711 0.0014719602 Hartree/Bohr -MM Grad( 11,:) = 0.0058563741 -0.0020721604 -0.0012500400 Hartree/Bohr -MM Grad( 12,:) = 0.0011666918 -0.0005276603 0.0001503173 Hartree/Bohr -MM Grad( 13,:) = -0.0018475864 -0.0000441056 0.0030407273 Hartree/Bohr -MM Grad( 14,:) = 0.0003060838 0.0010221439 -0.0022137719 Hartree/Bohr -MM Grad( 15,:) = 0.0016571182 -0.0010129675 -0.0009213709 Hartree/Bohr - - Computed energy and gradient with success. - Results from 4th calculation (changed coordinates of the QM region) -E = -76.0548152889 Hartrees -QM Grad( 1,:) = 0.0277853774 -0.0016369513 0.0124164694 Hartree/Bohr -QM Grad( 2,:) = -0.0340403806 -0.0300349490 -0.0126915118 Hartree/Bohr -QM Grad( 3,:) = -0.0022279424 0.0127779057 -0.0179219261 Hartree/Bohr -MM Grad( 1,:) = 0.0126910302 0.0153657018 0.0211217166 Hartree/Bohr -MM Grad( 2,:) = -0.0043962218 -0.0009158453 -0.0029765323 Hartree/Bohr -MM Grad( 3,:) = -0.0005489751 -0.0044261435 -0.0016275420 Hartree/Bohr -MM Grad( 4,:) = 0.0063032470 -0.0083947351 -0.0042624902 Hartree/Bohr -MM Grad( 5,:) = -0.0086801295 0.0164770036 0.0044569696 Hartree/Bohr -MM Grad( 6,:) = 0.0002138227 0.0024718914 0.0021228080 Hartree/Bohr -MM Grad( 7,:) = 0.0021354802 -0.0020712607 -0.0046028992 Hartree/Bohr -MM Grad( 8,:) = -0.0001875607 0.0001819157 0.0016904130 Hartree/Bohr -MM Grad( 9,:) = -0.0004087048 0.0012011603 0.0009645995 Hartree/Bohr -MM Grad( 10,:) = -0.0027383849 0.0011796748 0.0001970780 Hartree/Bohr -MM Grad( 11,:) = 0.0032142770 -0.0017502504 0.0000634532 Hartree/Bohr -MM Grad( 12,:) = 0.0005370657 -0.0004495643 0.0003930278 Hartree/Bohr -MM Grad( 13,:) = -0.0017946943 0.0016373740 0.0010381927 Hartree/Bohr -MM Grad( 14,:) = 0.0008848209 0.0000738152 -0.0013955991 Hartree/Bohr -MM Grad( 15,:) = 0.0012578729 -0.0016867429 0.0010137729 Hartree/Bohr - - Computed energy and gradient with success. - Results from 5th calculation (moved one molecule from the MM to the QM region) -E = -152.0466482595 Hartrees -QM Grad( 1,:) = -0.0481762818 0.0386359421 -0.0649893238 Hartree/Bohr -QM Grad( 2,:) = -0.0221519499 -0.0518790489 0.0102720182 Hartree/Bohr -QM Grad( 3,:) = 0.0889620924 0.0087778589 0.0683918958 Hartree/Bohr -QM Grad( 4,:) = -0.0642069330 0.0014927813 -0.0234297877 Hartree/Bohr -QM Grad( 5,:) = 0.0360936095 -0.0166648014 0.0031886659 Hartree/Bohr -QM Grad( 6,:) = 0.0073688899 0.0109374893 0.0029561339 Hartree/Bohr -MM Grad( 1,:) = 0.0063287824 -0.0099815554 -0.0066613769 Hartree/Bohr -MM Grad( 2,:) = -0.0091753422 0.0174866167 0.0090412338 Hartree/Bohr -MM Grad( 3,:) = 0.0009354336 0.0034408430 0.0026878493 Hartree/Bohr -MM Grad( 4,:) = 0.0009502041 0.0024136339 -0.0037967466 Hartree/Bohr -MM Grad( 5,:) = -0.0001064815 -0.0014104380 0.0008989851 Hartree/Bohr -MM Grad( 6,:) = -0.0000558684 -0.0000269082 0.0010201606 Hartree/Bohr -MM Grad( 7,:) = -0.0069575125 0.0001616051 0.0027486564 Hartree/Bohr -MM Grad( 8,:) = 0.0078235379 -0.0021736917 -0.0029912066 Hartree/Bohr -MM Grad( 9,:) = 0.0021163139 -0.0003867585 0.0000013238 Hartree/Bohr -MM Grad( 10,:) = -0.0011106775 0.0031665148 -0.0000889479 Hartree/Bohr -MM Grad( 11,:) = 0.0014790421 -0.0015913734 -0.0006122381 Hartree/Bohr -MM Grad( 12,:) = -0.0001168590 -0.0023987098 0.0013627048 Hartree/Bohr diff --git AmberTools/src/tcpb-cpp/api_examples/cpp/terachem.inp AmberTools/src/tcpb-cpp/api_examples/cpp/terachem.inp deleted file mode 100644 index 69314f0..0000000 --- AmberTools/src/tcpb-cpp/api_examples/cpp/terachem.inp +++ /dev/null @@ -1,9 +0,0 @@ -basis cc-pvdz -guess hcore -method rhf -run gradient - -charge 0 -spinmult 1 - -precision double diff --git AmberTools/src/tcpb-cpp/api_examples/cpp/test_api.cpp AmberTools/src/tcpb-cpp/api_examples/cpp/test_api.cpp deleted file mode 100644 index 2a54388..0000000 --- AmberTools/src/tcpb-cpp/api_examples/cpp/test_api.cpp +++ /dev/null @@ -1,321 +0,0 @@ -/** \file test_api.cpp - * \brief Example of API use - */ - -#include - -#include - -#define BohrToAng 0.52917724924 - -int main(int argc, char** argv) { - - double totenergy; - - // Set information about the server - char host[80] = "localhost"; - int port = 12345; - - // Other input variables - char tcfile[256] = "terachem.inp"; - - // Set global treatment - int globaltreatment = 0; - - // Information about initial QM region - int numqmatoms = 3; - char (*qmattypes)[5] = new char[numqmatoms][5] {"O","H","H"}; - - // Attempts to connect to the TeraChem server - printf(" Attempting to connect to TeraChem server using host %s and port %d.\n", host, port); - int status = -1; - tc_connect_(host, &port, &status); - if (status == 0) { - printf(" Successfully connected to TeraChem server.\n"); - } else if (status == 1) { - printf(" ERROR: Connection to TeraChem server failed!\n"); - return 1; - } else if (status == 2) { - printf(" ERROR: Connection to TeraChem server succeed, but the \n" - " server is not available!\n"); - return 1; - } else { - printf(" ERROR: Status on tc_connect function is not recognized!\n"); - return 1; - } - - // Setup TeraChem - status = -1; - tc_setup_(tcfile,qmattypes,&numqmatoms,&status); - if (status == 0) { - printf(" TeraChem setup completed with success.\n"); - } else if (status == 1) { - printf(" ERROR: No options read from TeraChem input file!\n"); - return 1; - } else if (status == 2) { - printf(" ERROR: Failed to setup TeraChem.\n"); - return 1; - } else { - printf(" ERROR: Status on tc_setup function is not recognized!\n"); - return 1; - } - - // Set QM region coordinates - double* qmcoords = new double[3*numqmatoms] - { -4.4798000, -2.8400000, 4.2456000, - -4.8525000, -3.7649000, 4.3951000, - -3.6050000, -2.7568000, 4.9264000}; - double* qmgrad = new double[3*numqmatoms]; - for (int i=0; i < 3*numqmatoms; i++) { - qmcoords[i] /= BohrToAng; - } - - // No MM region at the moment - int nummmatoms = 0; - - // Compute energy and gradient - printf("\n"); - status = -1; - tc_compute_energy_gradient_(qmattypes,qmcoords,&numqmatoms,&totenergy,qmgrad,nullptr,nullptr,&nummmatoms,nullptr,&globaltreatment,&status); - if (status == 0) { - printf(" Computed energy and gradient with success.\n"); - } else if (status == 1) { - printf(" ERROR: Mismatch in the variables passed to the function to compute energy and gradient!\n"); - return 1; - } else if (status == 2) { - printf(" ERROR: Problem to compute energy and gradient!\n"); - return 1; - } else { - printf(" ERROR: Status on tc_compute_energy_gradient function is not recognized!\n"); - return 1; - } - - // Print results - printf(" Results from 1st calculation (only one water molecule in the QM region)\n"); - printf("E = %16.10f Hartrees\n", totenergy); - for (int i=0; i < numqmatoms; i++) { - printf("QM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr\n",i+1,qmgrad[3*i], qmgrad[3*i+1], qmgrad[3*i+2]); - } - - // We now add an MM region - nummmatoms = 15; - double* mmcoords = new double[3*nummmatoms] - { -2.6793000, -2.1596000, 5.9264000, - -1.7944000, -2.5941000, 6.0208000, - -2.4543000, -1.2247000, 5.9247000, - -6.0739000, -0.8812700, 5.2104000, - -5.3910000, -1.5014000, 4.7942000, - -5.4189000, -0.3240900, 5.9375000, - -4.0898000, -5.6279000, 2.9956000, - -4.6091000, -5.6876000, 2.2341000, - -4.1166000, -6.5262000, 3.2888000, - -2.3448000, -2.6425000, 1.8190000, - -2.7846000, -3.1506000, 2.6164000, - -1.5986000, -3.2938000, 1.7252000, - -4.6456000, -4.4223000, 7.4705000, - -3.6650000, -4.5356000, 7.1235000, - -4.9759000, -3.5580000, 7.3041000 }; - for (int i=0; i < 3*nummmatoms; i++) { - mmcoords[i] /= BohrToAng; - } - double* mmcharges = new double[nummmatoms] - { -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417 }; - double* mmgrad = new double[3*nummmatoms]; - - // Compute energy and gradient - printf("\n"); - status = -1; - tc_compute_energy_gradient_(qmattypes,qmcoords,&numqmatoms,&totenergy,qmgrad,mmcoords,mmcharges,&nummmatoms,mmgrad,&globaltreatment,&status); - if (status == 0) { - printf(" Computed energy and gradient with success.\n"); - } else if (status == 1) { - printf(" ERROR: Mismatch in the variables passed to the function to compute energy and gradient!\n"); - return 1; - } else if (status == 2) { - printf(" ERROR: Problem to compute energy and gradient!\n"); - return 1; - } else { - printf(" ERROR: Status on tc_compute_energy_gradient function is not recognized!\n"); - return 1; - } - - // Print results - printf(" Results from 2nd calculation (one water molecule in the QM region and five in the MM region)\n"); - printf("E = %16.10f Hartrees\n", totenergy); - for (int i=0; i < numqmatoms; i++) { - printf("QM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr\n",i+1,qmgrad[3*i], qmgrad[3*i+1], qmgrad[3*i+2]); - } - for (int i=0; i < nummmatoms; i++) { - printf("MM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr\n",i+1,mmgrad[3*i], mmgrad[3*i+1], mmgrad[3*i+2]); - } - - // Compute energy and gradient - printf("\n"); - status = -1; - tc_compute_energy_gradient_(qmattypes,qmcoords,&numqmatoms,&totenergy,qmgrad,mmcoords,mmcharges,&nummmatoms,mmgrad,&globaltreatment,&status); - if (status == 0) { - printf(" Computed energy and gradient with success.\n"); - } else if (status == 1) { - printf(" ERROR: Mismatch in the variables passed to the function to compute energy and gradient!\n"); - return 1; - } else if (status == 2) { - printf(" ERROR: Problem to compute energy and gradient!\n"); - return 1; - } else { - printf(" ERROR: Status on tc_compute_energy_gradient function is not recognized!\n"); - return 1; - } - - // Print results - printf(" Results from 3rd calculation (just repeating the 2nd calculation)\n"); - printf("E = %16.10f Hartrees\n", totenergy); - for (int i=0; i < numqmatoms; i++) { - printf("QM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr\n",i+1,qmgrad[3*i], qmgrad[3*i+1], qmgrad[3*i+2]); - } - for (int i=0; i < nummmatoms; i++) { - printf("MM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr\n",i+1,mmgrad[3*i], mmgrad[3*i+1], mmgrad[3*i+2]); - } - - // Change coordinates of the QM region - delete[] qmcoords; - qmcoords = new double[3*numqmatoms] - { -4.4748000, -2.8700000, 4.5456000, - -4.8525000, -3.7649000, 4.3951000, - -3.6050000, -2.7568000, 4.9264000 }; - for (int i=0; i < 3*numqmatoms; i++) { - qmcoords[i] /= BohrToAng; - } - - // Compute energy and gradient - printf("\n"); - status = -1; - tc_compute_energy_gradient_(qmattypes,qmcoords,&numqmatoms,&totenergy,qmgrad,mmcoords,mmcharges,&nummmatoms,mmgrad,&globaltreatment,&status); - if (status == 0) { - printf(" Computed energy and gradient with success.\n"); - } else if (status == 1) { - printf(" ERROR: Mismatch in the variables passed to the function to compute energy and gradient!\n"); - return 1; - } else if (status == 2) { - printf(" ERROR: Problem to compute energy and gradient!\n"); - return 1; - } else { - printf(" ERROR: Status on tc_compute_energy_gradient function is not recognized!\n"); - return 1; - } - - // Print results - printf(" Results from 4th calculation (changed coordinates of the QM region)\n"); - printf("E = %16.10f Hartrees\n", totenergy); - for (int i=0; i < numqmatoms; i++) { - printf("QM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr\n",i+1,qmgrad[3*i], qmgrad[3*i+1], qmgrad[3*i+2]); - } - for (int i=0; i < nummmatoms; i++) { - printf("MM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr\n",i+1,mmgrad[3*i], mmgrad[3*i+1], mmgrad[3*i+2]); - } - - // Move one water molecule from the MM region to the QM region - numqmatoms = 6; - delete[] qmattypes; - qmattypes = new char[numqmatoms][5] {"O","H","H","O","H","H"}; - delete[] qmcoords; - qmcoords = new double[3*numqmatoms] - { -4.4798000, -2.8400000, 4.2456000, - -4.8525000, -3.7649000, 4.3951000, - -3.6050000, -2.7568000, 4.9264000, - -2.6793000, -2.1596000, 5.9264000, - -1.7944000, -2.5941000, 6.0208000, - -2.4543000, -1.2247000, 5.9247000 }; - delete[] qmgrad; - qmgrad = new double[3*numqmatoms]; - for (int i=0; i < 3*numqmatoms; i++) { - qmcoords[i] /= BohrToAng; - } - nummmatoms = 12; - delete[] mmcoords; - mmcoords = new double[3*nummmatoms] - { -6.0739000, -0.8812700, 5.2104000, - -5.3910000, -1.5014000, 4.7942000, - -5.4189000, -0.3240900, 5.9375000, - -4.0898000, -5.6279000, 2.9956000, - -4.6091000, -5.6876000, 2.2341000, - -4.1166000, -6.5262000, 3.2888000, - -2.3448000, -2.6425000, 1.8190000, - -2.7846000, -3.1506000, 2.6164000, - -1.5986000, -3.2938000, 1.7252000, - -4.6456000, -4.4223000, 7.4705000, - -3.6650000, -4.5356000, 7.1235000, - -4.9759000, -3.5580000, 7.3041000 }; - delete[] mmgrad; - mmgrad = new double[3*nummmatoms]; - for (int i=0; i < 3*nummmatoms; i++) { - mmcoords[i] /= BohrToAng; - } - delete[] mmcharges; - mmcharges = new double[nummmatoms] - { -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417 }; - - // Compute energy and gradient - printf("\n"); - status = -1; - tc_compute_energy_gradient_(qmattypes,qmcoords,&numqmatoms,&totenergy,qmgrad,mmcoords,mmcharges,&nummmatoms,mmgrad,&globaltreatment,&status); - if (status == 0) { - printf(" Computed energy and gradient with success.\n"); - } else if (status == 1) { - printf(" ERROR: Mismatch in the variables passed to the function to compute energy and gradient!\n"); - return 1; - } else if (status == 2) { - printf(" ERROR: Problem to compute energy and gradient!\n"); - return 1; - } else { - printf(" ERROR: Status on tc_compute_energy_gradient function is not recognized!\n"); - return 1; - } - - // Print results - printf(" Results from 5th calculation (moved one molecule from the MM to the QM region)\n"); - printf("E = %16.10f Hartrees\n", totenergy); - for (int i=0; i < numqmatoms; i++) { - printf("QM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr\n",i+1,qmgrad[3*i], qmgrad[3*i+1], qmgrad[3*i+2]); - } - for (int i=0; i < nummmatoms; i++) { - printf("MM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr\n",i+1,mmgrad[3*i], mmgrad[3*i+1], mmgrad[3*i+2]); - } - - // Finalizes variables on the TeraChem side - tc_finalize_(); - - // Delete variables that have been allocated on heap - delete[] qmattypes; - delete[] qmcoords; - delete[] qmgrad; - delete[] mmcoords; - delete[] mmcharges; - delete[] mmgrad; - - return 0; -} diff --git AmberTools/src/tcpb-cpp/api_examples/fortran/Makefile AmberTools/src/tcpb-cpp/api_examples/fortran/Makefile deleted file mode 100644 index 34fcf13..0000000 --- AmberTools/src/tcpb-cpp/api_examples/fortran/Makefile +++ /dev/null @@ -1,13 +0,0 @@ -# This Makefile assumes you have installed the C++ TCPB client with make install -# and added the lib and include folders to your environment - -include ../../config.h - -LIBS=-L$(LIBDIR) -ltcpb - -test_api_fortran: test_api.F90 - $(FC) $(FFLAGS) $(LIBS) -o $@ $< - -.PHONY: clean -clean: - @rm -v test_api_fortran diff --git AmberTools/src/tcpb-cpp/api_examples/fortran/reference.log AmberTools/src/tcpb-cpp/api_examples/fortran/reference.log deleted file mode 100644 index 6a52cad..0000000 --- AmberTools/src/tcpb-cpp/api_examples/fortran/reference.log +++ /dev/null @@ -1,98 +0,0 @@ - Attempting to connect to TeraChem server using host localhost and port 12345 . - Successfully connected to TeraChem server. - TeraChem setup completed with success. - - Computed energy and gradient with success. - Results from 1st calculation (only one water molecule in the QM region) -E = -76.0022844544 Hartrees -QM Grad( 1,:) = -0.0642463980 0.0371034421 -0.0713540769 Hartree/Bohr -QM Grad( 2,:) = -0.0266141637 -0.0518086391 0.0036397418 Hartree/Bohr -QM Grad( 3,:) = 0.0908605618 0.0147051970 0.0677143350 Hartree/Bohr - - Computed energy and gradient with success. - Results from 2nd calculation (one water molecule in the QM region and five in the MM region) -E = -76.0387136201 Hartrees -QM Grad( 1,:) = -0.0620229271 0.0306042943 -0.0738584016 Hartree/Bohr -QM Grad( 2,:) = -0.0247730873 -0.0505936308 0.0075343381 Hartree/Bohr -QM Grad( 3,:) = 0.0745816528 0.0010694430 0.0466698947 Hartree/Bohr -MM Grad( 1,:) = 0.0168460146 0.0176625994 0.0202798048 Hartree/Bohr -MM Grad( 2,:) = -0.0052857623 -0.0011172724 -0.0025479307 Hartree/Bohr -MM Grad( 3,:) = -0.0012305920 -0.0049104978 -0.0011060955 Hartree/Bohr -MM Grad( 4,:) = 0.0047910607 -0.0062894775 -0.0061427873 Hartree/Bohr -MM Grad( 5,:) = -0.0070490574 0.0137660690 0.0088585533 Hartree/Bohr -MM Grad( 6,:) = 0.0004543010 0.0013874752 0.0023238939 Hartree/Bohr -MM Grad( 7,:) = 0.0018573907 0.0001200172 -0.0051518439 Hartree/Bohr -MM Grad( 8,:) = -0.0002598900 -0.0006551838 0.0015615262 Hartree/Bohr -MM Grad( 9,:) = -0.0003799401 0.0007765589 0.0013011774 Hartree/Bohr -MM Grad( 10,:) = -0.0046678908 0.0008143731 0.0014719501 Hartree/Bohr -MM Grad( 11,:) = 0.0058564215 -0.0020721506 -0.0012500193 Hartree/Bohr -MM Grad( 12,:) = 0.0011666958 -0.0005276604 0.0001503221 Hartree/Bohr -MM Grad( 13,:) = -0.0018475363 -0.0000440524 0.0030407459 Hartree/Bohr -MM Grad( 14,:) = 0.0003060683 0.0010221057 -0.0022137623 Hartree/Bohr -MM Grad( 15,:) = 0.0016570779 -0.0010130103 -0.0009213657 Hartree/Bohr - - Computed energy and gradient with success. - Results from 3rd calculation (just repeating the 2nd calculation) -E = -76.0387136124 Hartrees -QM Grad( 1,:) = -0.0620194224 0.0305990472 -0.0738538336 Hartree/Bohr -QM Grad( 2,:) = -0.0247672481 -0.0505865888 0.0075303582 Hartree/Bohr -QM Grad( 3,:) = 0.0745721809 0.0010677291 0.0466694660 Hartree/Bohr -MM Grad( 1,:) = 0.0168462242 0.0176626629 0.0202796602 Hartree/Bohr -MM Grad( 2,:) = -0.0052857901 -0.0011172756 -0.0025478975 Hartree/Bohr -MM Grad( 3,:) = -0.0012306275 -0.0049105037 -0.0011060668 Hartree/Bohr -MM Grad( 4,:) = 0.0047909573 -0.0062894161 -0.0061427556 Hartree/Bohr -MM Grad( 5,:) = -0.0070489469 0.0137659194 0.0088585058 Hartree/Bohr -MM Grad( 6,:) = 0.0004543197 0.0013874419 0.0023238764 Hartree/Bohr -MM Grad( 7,:) = 0.0018573313 0.0001199891 -0.0051518122 Hartree/Bohr -MM Grad( 8,:) = -0.0002598724 -0.0006551795 0.0015615109 Hartree/Bohr -MM Grad( 9,:) = -0.0003799223 0.0007765528 0.0013011662 Hartree/Bohr -MM Grad( 10,:) = -0.0046678654 0.0008143711 0.0014719602 Hartree/Bohr -MM Grad( 11,:) = 0.0058563741 -0.0020721604 -0.0012500400 Hartree/Bohr -MM Grad( 12,:) = 0.0011666918 -0.0005276603 0.0001503173 Hartree/Bohr -MM Grad( 13,:) = -0.0018475864 -0.0000441056 0.0030407273 Hartree/Bohr -MM Grad( 14,:) = 0.0003060838 0.0010221439 -0.0022137719 Hartree/Bohr -MM Grad( 15,:) = 0.0016571182 -0.0010129675 -0.0009213709 Hartree/Bohr - - Computed energy and gradient with success. - Results from 4th calculation (changed coordinates of the QM region) -E = -76.0548152889 Hartrees -QM Grad( 1,:) = 0.0277853774 -0.0016369513 0.0124164694 Hartree/Bohr -QM Grad( 2,:) = -0.0340403806 -0.0300349490 -0.0126915118 Hartree/Bohr -QM Grad( 3,:) = -0.0022279424 0.0127779057 -0.0179219261 Hartree/Bohr -MM Grad( 1,:) = 0.0126910302 0.0153657018 0.0211217166 Hartree/Bohr -MM Grad( 2,:) = -0.0043962218 -0.0009158453 -0.0029765323 Hartree/Bohr -MM Grad( 3,:) = -0.0005489751 -0.0044261435 -0.0016275420 Hartree/Bohr -MM Grad( 4,:) = 0.0063032470 -0.0083947351 -0.0042624902 Hartree/Bohr -MM Grad( 5,:) = -0.0086801295 0.0164770036 0.0044569696 Hartree/Bohr -MM Grad( 6,:) = 0.0002138227 0.0024718914 0.0021228080 Hartree/Bohr -MM Grad( 7,:) = 0.0021354802 -0.0020712607 -0.0046028992 Hartree/Bohr -MM Grad( 8,:) = -0.0001875607 0.0001819157 0.0016904130 Hartree/Bohr -MM Grad( 9,:) = -0.0004087048 0.0012011603 0.0009645995 Hartree/Bohr -MM Grad( 10,:) = -0.0027383849 0.0011796748 0.0001970780 Hartree/Bohr -MM Grad( 11,:) = 0.0032142770 -0.0017502504 0.0000634532 Hartree/Bohr -MM Grad( 12,:) = 0.0005370657 -0.0004495643 0.0003930278 Hartree/Bohr -MM Grad( 13,:) = -0.0017946943 0.0016373740 0.0010381927 Hartree/Bohr -MM Grad( 14,:) = 0.0008848209 0.0000738152 -0.0013955991 Hartree/Bohr -MM Grad( 15,:) = 0.0012578729 -0.0016867429 0.0010137729 Hartree/Bohr - - Computed energy and gradient with success. - Results from 5th calculation (moved one molecule from the MM to the QM region) -E = -152.0466482595 Hartrees -QM Grad( 1,:) = -0.0481762818 0.0386359421 -0.0649893238 Hartree/Bohr -QM Grad( 2,:) = -0.0221519499 -0.0518790489 0.0102720182 Hartree/Bohr -QM Grad( 3,:) = 0.0889620924 0.0087778589 0.0683918958 Hartree/Bohr -QM Grad( 4,:) = -0.0642069330 0.0014927813 -0.0234297877 Hartree/Bohr -QM Grad( 5,:) = 0.0360936095 -0.0166648014 0.0031886659 Hartree/Bohr -QM Grad( 6,:) = 0.0073688899 0.0109374893 0.0029561339 Hartree/Bohr -MM Grad( 1,:) = 0.0063287824 -0.0099815554 -0.0066613769 Hartree/Bohr -MM Grad( 2,:) = -0.0091753422 0.0174866167 0.0090412338 Hartree/Bohr -MM Grad( 3,:) = 0.0009354336 0.0034408430 0.0026878493 Hartree/Bohr -MM Grad( 4,:) = 0.0009502041 0.0024136339 -0.0037967466 Hartree/Bohr -MM Grad( 5,:) = -0.0001064815 -0.0014104380 0.0008989851 Hartree/Bohr -MM Grad( 6,:) = -0.0000558684 -0.0000269082 0.0010201606 Hartree/Bohr -MM Grad( 7,:) = -0.0069575125 0.0001616051 0.0027486564 Hartree/Bohr -MM Grad( 8,:) = 0.0078235379 -0.0021736917 -0.0029912066 Hartree/Bohr -MM Grad( 9,:) = 0.0021163139 -0.0003867585 0.0000013238 Hartree/Bohr -MM Grad( 10,:) = -0.0011106775 0.0031665148 -0.0000889479 Hartree/Bohr -MM Grad( 11,:) = 0.0014790421 -0.0015913734 -0.0006122381 Hartree/Bohr -MM Grad( 12,:) = -0.0001168590 -0.0023987098 0.0013627048 Hartree/Bohr diff --git AmberTools/src/tcpb-cpp/api_examples/fortran/terachem.inp AmberTools/src/tcpb-cpp/api_examples/fortran/terachem.inp deleted file mode 100644 index 69314f0..0000000 --- AmberTools/src/tcpb-cpp/api_examples/fortran/terachem.inp +++ /dev/null @@ -1,9 +0,0 @@ -basis cc-pvdz -guess hcore -method rhf -run gradient - -charge 0 -spinmult 1 - -precision double diff --git AmberTools/src/tcpb-cpp/api_examples/fortran/test_api.F90 AmberTools/src/tcpb-cpp/api_examples/fortran/test_api.F90 deleted file mode 100644 index 41bb312..0000000 --- AmberTools/src/tcpb-cpp/api_examples/fortran/test_api.F90 +++ /dev/null @@ -1,316 +0,0 @@ -!**************************************************** -! Program for testing TCPB working as an API library -! Implemented by: Vinicius Wilian D. Cruzeiro -!**************************************************** - -program test_api - -implicit none - -character(len=80) :: host -character(len=256) :: tcfile -integer :: port, status, globaltreatment -integer :: numqmatoms, nummmatoms -integer :: i -double precision :: totenergy -character(len=5), allocatable :: qmattypes(:) -double precision, allocatable :: qmcoords(:), mmcoords(:), mmcharges(:), qmgrad(:), mmgrad(:) -double precision, parameter :: BohrToAng = 0.52917724924d0 - -! Set information about the server -host = "localhost" -port = 12345 - -! Other input variables -tcfile = "terachem.inp" -tcfile = trim(tcfile)//CHAR(0) - -! Set global treatment -globaltreatment = 0 - -! Information about initial QM region -numqmatoms = 3 -allocate(qmattypes(numqmatoms)) -qmattypes = (/ "O","H","H" /) -do i =1, numqmatoms - qmattypes(i)=trim(qmattypes(i))//CHAR(0) -end do - -! Attempts to connect to the TeraChem server -write (*,*) "Attempting to connect to TeraChem server using host ", & - trim(host), " and port ", port, "." -status = -1 -call tc_connect(trim(host)//CHAR(0), port, status) -if (status == 0) then - write (*,*) "Successfully connected to TeraChem server." -else if (status == 1) then - write (*,*) "ERROR: Connection to TeraChem server failed!" - STOP -else if (status == 2) then - write (*,*) "ERROR: Connection to TeraChem server succeed, but the ", & - " server is not available!" - STOP -else - write (*,*) "ERROR: Status on tc_connect function is not recognized!" - STOP -end if - -! Setup TeraChem -status = -1 -call tc_setup(tcfile,qmattypes,numqmatoms,status) -if (status == 0) then - write (*,*) "TeraChem setup completed with success." -else if (status == 1) then - write (*,*) "ERROR: No options read from TeraChem input file!" - STOP -else if (status == 2) then - write (*,*) "ERROR: Failed to setup TeraChem." - STOP -else - write (*,*) "ERROR: Status on tc_setup function is not recognized!" - STOP -end if - -! Set QM region coordinates -allocate(qmcoords(3*numqmatoms),qmgrad(3*numqmatoms)) -qmcoords = (/ -4.4798000d0, -2.8400000d0, 4.2456000d0,& - -4.8525000d0, -3.7649000d0, 4.3951000d0,& - -3.6050000d0, -2.7568000d0, 4.9264000d0 /) -do i =1, 3*numqmatoms - qmcoords(i)=qmcoords(i)/BohrToAng -end do - -! No MM region at the moment -nummmatoms = 0 - -! Compute energy and gradient -write (*,*) "" -status = -1 -call tc_compute_energy_gradient(qmattypes,qmcoords,numqmatoms,totenergy,qmgrad,mmcoords,mmcharges,nummmatoms,mmgrad,globaltreatment,status) -if (status == 0) then - write (*,*) "Computed energy and gradient with success." -else if (status == 1) then - write (*,*) "ERROR: Mismatch in the variables passed to the function to compute energy and gradient!" - STOP -else if (status == 2) then - write (*,*) "ERROR: Problem to compute energy and gradient!" - STOP -else - write (*,*) "ERROR: Status on tc_compute_energy_gradient function is not recognized!" - STOP -end if - -! Print results -write (*,*) "Results from 1st calculation (only one water molecule in the QM region)" -write (*,'(a,f16.10,a)') "E = ", totenergy, " Hartrees" -do i =1, numqmatoms - write (*,'(a,i3,a,3f16.10,a)') "QM Grad(",i,",:) = ",qmgrad(3*(i-1)+1), qmgrad(3*(i-1)+2), qmgrad(3*(i-1)+3), " Hartree/Bohr" -end do - -! We now add an MM region -nummmatoms = 15 -allocate(mmcoords(3*nummmatoms),mmcharges(nummmatoms),mmgrad(3*nummmatoms)) -mmcoords = (/ -2.6793000d0, -2.1596000d0, 5.9264000d0,& - -1.7944000d0, -2.5941000d0, 6.0208000d0,& - -2.4543000d0, -1.2247000d0, 5.9247000d0,& - -6.0739000d0, -0.8812700d0, 5.2104000d0,& - -5.3910000d0, -1.5014000d0, 4.7942000d0,& - -5.4189000d0, -0.3240900d0, 5.9375000d0,& - -4.0898000d0, -5.6279000d0, 2.9956000d0,& - -4.6091000d0, -5.6876000d0, 2.2341000d0,& - -4.1166000d0, -6.5262000d0, 3.2888000d0,& - -2.3448000d0, -2.6425000d0, 1.8190000d0,& - -2.7846000d0, -3.1506000d0, 2.6164000d0,& - -1.5986000d0, -3.2938000d0, 1.7252000d0,& - -4.6456000d0, -4.4223000d0, 7.4705000d0,& - -3.6650000d0, -4.5356000d0, 7.1235000d0,& - -4.9759000d0, -3.5580000d0, 7.3041000d0 /) -do i =1, 3*nummmatoms - mmcoords(i)=mmcoords(i)/BohrToAng -end do -mmcharges = (/ -0.834d0,& - 0.417d0,& - 0.417d0,& - -0.834d0,& - 0.417d0,& - 0.417d0,& - -0.834d0,& - 0.417d0,& - 0.417d0,& - -0.834d0,& - 0.417d0,& - 0.417d0,& - -0.834d0,& - 0.417d0,& - 0.417d0 /) - -! Compute energy and gradient -write (*,*) "" -status = -1 -call tc_compute_energy_gradient(qmattypes,qmcoords,numqmatoms,totenergy,qmgrad,mmcoords,mmcharges,nummmatoms,mmgrad,globaltreatment,status) -if (status == 0) then - write (*,*) "Computed energy and gradient with success." -else if (status == 1) then - write (*,*) "ERROR: Mismatch in the variables passed to the function to compute energy and gradient!" - STOP -else if (status == 2) then - write (*,*) "ERROR: Problem to compute energy and gradient!" - STOP -else - write (*,*) "ERROR: Status on tc_compute_energy_gradient function is not recognized!" - STOP -end if - -! Print results -write (*,*) "Results from 2nd calculation (one water molecule in the QM region and five in the MM region)" -write (*,'(a,f16.10,a)') "E = ", totenergy, " Hartrees" -do i =1, numqmatoms - write (*,'(a,i3,a,3f16.10,a)') "QM Grad(",i,",:) = ",qmgrad(3*(i-1)+1), qmgrad(3*(i-1)+2), qmgrad(3*(i-1)+3), " Hartree/Bohr" -end do -do i =1, nummmatoms - write (*,'(a,i3,a,3f16.10,a)') "MM Grad(",i,",:) = ",mmgrad(3*(i-1)+1), mmgrad(3*(i-1)+2), mmgrad(3*(i-1)+3), " Hartree/Bohr" -end do - -! Compute energy and gradient -write (*,*) "" -status = -1 -call tc_compute_energy_gradient(qmattypes,qmcoords,numqmatoms,totenergy,qmgrad,mmcoords,mmcharges,nummmatoms,mmgrad,globaltreatment,status) -if (status == 0) then - write (*,*) "Computed energy and gradient with success." -else if (status == 1) then - write (*,*) "ERROR: Mismatch in the variables passed to the function to compute energy and gradient!" - STOP -else if (status == 2) then - write (*,*) "ERROR: Problem to compute energy and gradient!" - STOP -else - write (*,*) "ERROR: Status on tc_compute_energy_gradient function is not recognized!" - STOP -end if - -! Print results -write (*,*) "Results from 3rd calculation (just repeating the 2nd calculation)" -write (*,'(a,f16.10,a)') "E = ", totenergy, " Hartrees" -do i =1, numqmatoms - write (*,'(a,i3,a,3f16.10,a)') "QM Grad(",i,",:) = ",qmgrad(3*(i-1)+1), qmgrad(3*(i-1)+2), qmgrad(3*(i-1)+3), " Hartree/Bohr" -end do -do i =1, nummmatoms - write (*,'(a,i3,a,3f16.10,a)') "MM Grad(",i,",:) = ",mmgrad(3*(i-1)+1), mmgrad(3*(i-1)+2), mmgrad(3*(i-1)+3), " Hartree/Bohr" -end do - -! Change coordinates of the QM region -qmcoords = (/ -4.4748000d0, -2.8700000d0, 4.5456000d0,& - -4.8525000d0, -3.7649000d0, 4.3951000d0,& - -3.6050000d0, -2.7568000d0, 4.9264000d0 /) -do i =1, 3*numqmatoms - qmcoords(i)=qmcoords(i)/BohrToAng -end do - -! Compute energy and gradient -write (*,*) "" -status = -1 -call tc_compute_energy_gradient(qmattypes,qmcoords,numqmatoms,totenergy,qmgrad,mmcoords,mmcharges,nummmatoms,mmgrad,globaltreatment,status) -if (status == 0) then - write (*,*) "Computed energy and gradient with success." -else if (status == 1) then - write (*,*) "ERROR: Mismatch in the variables passed to the function to compute energy and gradient!" - STOP -else if (status == 2) then - write (*,*) "ERROR: Problem to compute energy and gradient!" - STOP -else - write (*,*) "ERROR: Status on tc_compute_energy_gradient function is not recognized!" - STOP -end if - -! Print results -write (*,*) "Results from 4th calculation (changed coordinates of the QM region)" -write (*,'(a,f16.10,a)') "E = ", totenergy, " Hartrees" -do i =1, numqmatoms - write (*,'(a,i3,a,3f16.10,a)') "QM Grad(",i,",:) = ",qmgrad(3*(i-1)+1), qmgrad(3*(i-1)+2), qmgrad(3*(i-1)+3), " Hartree/Bohr" -end do -do i =1, nummmatoms - write (*,'(a,i3,a,3f16.10,a)') "MM Grad(",i,",:) = ",mmgrad(3*(i-1)+1), mmgrad(3*(i-1)+2), mmgrad(3*(i-1)+3), " Hartree/Bohr" -end do - -! Move one water molecule from the MM region to the QM region -deallocate(qmattypes,qmcoords,qmgrad,mmcoords,mmcharges,mmgrad) -numqmatoms = 6 -allocate(qmattypes(numqmatoms),qmcoords(3*numqmatoms),qmgrad(3*numqmatoms)) -qmattypes = (/ "O","H","H","O","H","H" /) -do i =1, numqmatoms - qmattypes(i)=trim(qmattypes(i))//CHAR(0) -end do -qmcoords = (/ -4.4798000d0, -2.8400000d0, 4.2456000d0,& - -4.8525000d0, -3.7649000d0, 4.3951000d0,& - -3.6050000d0, -2.7568000d0, 4.9264000d0,& - -2.6793000d0, -2.1596000d0, 5.9264000d0,& - -1.7944000d0, -2.5941000d0, 6.0208000d0,& - -2.4543000d0, -1.2247000d0, 5.9247000d0 /) -do i =1, 3*numqmatoms - qmcoords(i)=qmcoords(i)/BohrToAng -end do -nummmatoms = 12 -allocate(mmcoords(3*nummmatoms),mmcharges(nummmatoms),mmgrad(3*nummmatoms)) -mmcoords = (/ -6.0739000d0, -0.8812700d0, 5.2104000d0,& - -5.3910000d0, -1.5014000d0, 4.7942000d0,& - -5.4189000d0, -0.3240900d0, 5.9375000d0,& - -4.0898000d0, -5.6279000d0, 2.9956000d0,& - -4.6091000d0, -5.6876000d0, 2.2341000d0,& - -4.1166000d0, -6.5262000d0, 3.2888000d0,& - -2.3448000d0, -2.6425000d0, 1.8190000d0,& - -2.7846000d0, -3.1506000d0, 2.6164000d0,& - -1.5986000d0, -3.2938000d0, 1.7252000d0,& - -4.6456000d0, -4.4223000d0, 7.4705000d0,& - -3.6650000d0, -4.5356000d0, 7.1235000d0,& - -4.9759000d0, -3.5580000d0, 7.3041000d0 /) -do i =1, 3*nummmatoms - mmcoords(i)=mmcoords(i)/BohrToAng -end do -mmcharges = (/ -0.834d0,& - 0.417d0,& - 0.417d0,& - -0.834d0,& - 0.417d0,& - 0.417d0,& - -0.834d0,& - 0.417d0,& - 0.417d0,& - -0.834d0,& - 0.417d0,& - 0.417d0 /) - -! Compute energy and gradient -write (*,*) "" -status = -1 -call tc_compute_energy_gradient(qmattypes,qmcoords,numqmatoms,totenergy,qmgrad,mmcoords,mmcharges,nummmatoms,mmgrad,globaltreatment,status) -if (status == 0) then - write (*,*) "Computed energy and gradient with success." -else if (status == 1) then - write (*,*) "ERROR: Mismatch in the variables passed to the function to compute energy and gradient!" - STOP -else if (status == 2) then - write (*,*) "ERROR: Problem to compute energy and gradient!" - STOP -else - write (*,*) "ERROR: Status on tc_compute_energy_gradient function is not recognized!" - STOP -end if - -! Print results -write (*,*) "Results from 5th calculation (moved one molecule from the MM to the QM region)" -write (*,'(a,f16.10,a)') "E = ", totenergy, " Hartrees" -do i =1, numqmatoms - write (*,'(a,i3,a,3f16.10,a)') "QM Grad(",i,",:) = ",qmgrad(3*(i-1)+1), qmgrad(3*(i-1)+2), qmgrad(3*(i-1)+3), " Hartree/Bohr" -end do -do i =1, nummmatoms - write (*,'(a,i3,a,3f16.10,a)') "MM Grad(",i,",:) = ",mmgrad(3*(i-1)+1), mmgrad(3*(i-1)+2), mmgrad(3*(i-1)+3), " Hartree/Bohr" -end do - -! Finalizes variables on the TeraChem side -call tc_finalize() - -! Deallocate variables that have been allocated -deallocate(qmattypes,qmcoords,qmgrad,mmcoords,mmcharges,mmgrad) - -end program test_api diff --git AmberTools/src/tcpb-cpp/api_examples/python/reference.log AmberTools/src/tcpb-cpp/api_examples/python/reference.log deleted file mode 100644 index eaea166..0000000 --- AmberTools/src/tcpb-cpp/api_examples/python/reference.log +++ /dev/null @@ -1,98 +0,0 @@ - Attempting to connect to TeraChem server using host localhost and port 12345. - Successfully connected to TeraChem server. - TeraChem setup completed with success. - - Computed energy and gradient with success. - Results from 1st calculation (only one water molecule in the QM region) -E = -76.0022844544 Hartrees -QM Grad( 1,:) = -0.0642463980 0.0371034421 -0.0713540769 Hartree/Bohr -QM Grad( 2,:) = -0.0266141637 -0.0518086391 0.0036397418 Hartree/Bohr -QM Grad( 3,:) = 0.0908605618 0.0147051970 0.0677143350 Hartree/Bohr - - Computed energy and gradient with success. - Results from 2nd calculation (one water molecule in the QM region and five in the MM region) -E = -76.0387136201 Hartrees -QM Grad( 1,:) = -0.0620229271 0.0306042943 -0.0738584016 Hartree/Bohr -QM Grad( 2,:) = -0.0247730873 -0.0505936308 0.0075343381 Hartree/Bohr -QM Grad( 3,:) = 0.0745816528 0.0010694430 0.0466698947 Hartree/Bohr -MM Grad( 1,:) = 0.0168460146 0.0176625994 0.0202798048 Hartree/Bohr -MM Grad( 2,:) = -0.0052857623 -0.0011172724 -0.0025479307 Hartree/Bohr -MM Grad( 3,:) = -0.0012305920 -0.0049104978 -0.0011060955 Hartree/Bohr -MM Grad( 4,:) = 0.0047910607 -0.0062894775 -0.0061427873 Hartree/Bohr -MM Grad( 5,:) = -0.0070490574 0.0137660690 0.0088585533 Hartree/Bohr -MM Grad( 6,:) = 0.0004543010 0.0013874752 0.0023238939 Hartree/Bohr -MM Grad( 7,:) = 0.0018573907 0.0001200172 -0.0051518439 Hartree/Bohr -MM Grad( 8,:) = -0.0002598900 -0.0006551838 0.0015615262 Hartree/Bohr -MM Grad( 9,:) = -0.0003799401 0.0007765589 0.0013011774 Hartree/Bohr -MM Grad( 10,:) = -0.0046678908 0.0008143731 0.0014719501 Hartree/Bohr -MM Grad( 11,:) = 0.0058564215 -0.0020721506 -0.0012500193 Hartree/Bohr -MM Grad( 12,:) = 0.0011666958 -0.0005276604 0.0001503221 Hartree/Bohr -MM Grad( 13,:) = -0.0018475363 -0.0000440524 0.0030407459 Hartree/Bohr -MM Grad( 14,:) = 0.0003060683 0.0010221057 -0.0022137623 Hartree/Bohr -MM Grad( 15,:) = 0.0016570779 -0.0010130103 -0.0009213657 Hartree/Bohr - - Computed energy and gradient with success. - Results from 3rd calculation (just repeating the 2nd calculation) -E = -76.0387136124 Hartrees -QM Grad( 1,:) = -0.0620194224 0.0305990472 -0.0738538336 Hartree/Bohr -QM Grad( 2,:) = -0.0247672481 -0.0505865888 0.0075303582 Hartree/Bohr -QM Grad( 3,:) = 0.0745721809 0.0010677291 0.0466694660 Hartree/Bohr -MM Grad( 1,:) = 0.0168462242 0.0176626629 0.0202796602 Hartree/Bohr -MM Grad( 2,:) = -0.0052857901 -0.0011172756 -0.0025478975 Hartree/Bohr -MM Grad( 3,:) = -0.0012306275 -0.0049105037 -0.0011060668 Hartree/Bohr -MM Grad( 4,:) = 0.0047909573 -0.0062894161 -0.0061427556 Hartree/Bohr -MM Grad( 5,:) = -0.0070489469 0.0137659194 0.0088585058 Hartree/Bohr -MM Grad( 6,:) = 0.0004543197 0.0013874419 0.0023238764 Hartree/Bohr -MM Grad( 7,:) = 0.0018573313 0.0001199891 -0.0051518122 Hartree/Bohr -MM Grad( 8,:) = -0.0002598724 -0.0006551795 0.0015615109 Hartree/Bohr -MM Grad( 9,:) = -0.0003799223 0.0007765528 0.0013011662 Hartree/Bohr -MM Grad( 10,:) = -0.0046678654 0.0008143711 0.0014719602 Hartree/Bohr -MM Grad( 11,:) = 0.0058563741 -0.0020721604 -0.0012500400 Hartree/Bohr -MM Grad( 12,:) = 0.0011666918 -0.0005276603 0.0001503173 Hartree/Bohr -MM Grad( 13,:) = -0.0018475864 -0.0000441056 0.0030407273 Hartree/Bohr -MM Grad( 14,:) = 0.0003060838 0.0010221439 -0.0022137719 Hartree/Bohr -MM Grad( 15,:) = 0.0016571182 -0.0010129675 -0.0009213709 Hartree/Bohr - - Computed energy and gradient with success. - Results from 4th calculation (changed coordinates of the QM region) -E = -76.0548152889 Hartrees -QM Grad( 1,:) = 0.0277853774 -0.0016369513 0.0124164694 Hartree/Bohr -QM Grad( 2,:) = -0.0340403806 -0.0300349490 -0.0126915118 Hartree/Bohr -QM Grad( 3,:) = -0.0022279424 0.0127779057 -0.0179219261 Hartree/Bohr -MM Grad( 1,:) = 0.0126910302 0.0153657018 0.0211217166 Hartree/Bohr -MM Grad( 2,:) = -0.0043962218 -0.0009158453 -0.0029765323 Hartree/Bohr -MM Grad( 3,:) = -0.0005489751 -0.0044261435 -0.0016275420 Hartree/Bohr -MM Grad( 4,:) = 0.0063032470 -0.0083947351 -0.0042624902 Hartree/Bohr -MM Grad( 5,:) = -0.0086801295 0.0164770036 0.0044569696 Hartree/Bohr -MM Grad( 6,:) = 0.0002138227 0.0024718914 0.0021228080 Hartree/Bohr -MM Grad( 7,:) = 0.0021354802 -0.0020712607 -0.0046028992 Hartree/Bohr -MM Grad( 8,:) = -0.0001875607 0.0001819157 0.0016904130 Hartree/Bohr -MM Grad( 9,:) = -0.0004087048 0.0012011603 0.0009645995 Hartree/Bohr -MM Grad( 10,:) = -0.0027383849 0.0011796748 0.0001970780 Hartree/Bohr -MM Grad( 11,:) = 0.0032142770 -0.0017502504 0.0000634532 Hartree/Bohr -MM Grad( 12,:) = 0.0005370657 -0.0004495643 0.0003930278 Hartree/Bohr -MM Grad( 13,:) = -0.0017946943 0.0016373740 0.0010381927 Hartree/Bohr -MM Grad( 14,:) = 0.0008848209 0.0000738152 -0.0013955991 Hartree/Bohr -MM Grad( 15,:) = 0.0012578729 -0.0016867429 0.0010137729 Hartree/Bohr - - Computed energy and gradient with success. - Results from 5th calculation (moved one molecule from the MM to the QM region) -E = -152.0466482595 Hartrees -QM Grad( 1,:) = -0.0481762818 0.0386359421 -0.0649893238 Hartree/Bohr -QM Grad( 2,:) = -0.0221519499 -0.0518790489 0.0102720182 Hartree/Bohr -QM Grad( 3,:) = 0.0889620924 0.0087778589 0.0683918958 Hartree/Bohr -QM Grad( 4,:) = -0.0642069330 0.0014927813 -0.0234297877 Hartree/Bohr -QM Grad( 5,:) = 0.0360936095 -0.0166648014 0.0031886659 Hartree/Bohr -QM Grad( 6,:) = 0.0073688899 0.0109374893 0.0029561339 Hartree/Bohr -MM Grad( 1,:) = 0.0063287824 -0.0099815554 -0.0066613769 Hartree/Bohr -MM Grad( 2,:) = -0.0091753422 0.0174866167 0.0090412338 Hartree/Bohr -MM Grad( 3,:) = 0.0009354336 0.0034408430 0.0026878493 Hartree/Bohr -MM Grad( 4,:) = 0.0009502041 0.0024136339 -0.0037967466 Hartree/Bohr -MM Grad( 5,:) = -0.0001064815 -0.0014104380 0.0008989851 Hartree/Bohr -MM Grad( 6,:) = -0.0000558684 -0.0000269082 0.0010201606 Hartree/Bohr -MM Grad( 7,:) = -0.0069575125 0.0001616051 0.0027486564 Hartree/Bohr -MM Grad( 8,:) = 0.0078235379 -0.0021736917 -0.0029912066 Hartree/Bohr -MM Grad( 9,:) = 0.0021163139 -0.0003867585 0.0000013238 Hartree/Bohr -MM Grad( 10,:) = -0.0011106775 0.0031665148 -0.0000889479 Hartree/Bohr -MM Grad( 11,:) = 0.0014790421 -0.0015913734 -0.0006122381 Hartree/Bohr -MM Grad( 12,:) = -0.0001168590 -0.0023987098 0.0013627048 Hartree/Bohr diff --git AmberTools/src/tcpb-cpp/api_examples/python/terachem.inp AmberTools/src/tcpb-cpp/api_examples/python/terachem.inp deleted file mode 100644 index 69314f0..0000000 --- AmberTools/src/tcpb-cpp/api_examples/python/terachem.inp +++ /dev/null @@ -1,9 +0,0 @@ -basis cc-pvdz -guess hcore -method rhf -run gradient - -charge 0 -spinmult 1 - -precision double diff --git AmberTools/src/tcpb-cpp/api_examples/python/test_api.py AmberTools/src/tcpb-cpp/api_examples/python/test_api.py deleted file mode 100644 index 89f467f..0000000 --- AmberTools/src/tcpb-cpp/api_examples/python/test_api.py +++ /dev/null @@ -1,259 +0,0 @@ -import sys -# Load tcpb_wrapper.py -try: - import pytcpb as tc -except: - print("ERROR: Failed to import pytcpb in test_api.py") - sys.exit(1) - -BohrToAng = 0.52917724924 - -# Set information about the server -host = "localhost" -port = 12345 - -# Other input variables -tcfile = "terachem.inp" - -# Set global treatment -globaltreatment = 0 - -# Information about initial QM region -qmattypes = ["O","H","H"] - -# Attempts to connect to the TeraChem server -print(" Attempting to connect to TeraChem server using host %s and port %d."%(host, port)) -status = tc.connect(host, port) -if (status == 0): - print(" Successfully connected to TeraChem server.") -elif (status == 1): - print(" ERROR: Connection to TeraChem server failed!") - sys.exit(1) -elif (status == 2): - print(" ERROR: Connection to TeraChem server succeed, but the \n", - " server is not available!") - sys.exit(1) -else: - print(" ERROR: Status on tc.connect function is not recognized!") - sys.exit(1) - -# Setup TeraChem -status = tc.setup(tcfile,qmattypes) -if (status == 0): - print(" TeraChem setup completed with success.") -elif (status == 1): - print(" ERROR: No options read from TeraChem input file!") - sys.exit(1) -elif (status == 2): - printf(" ERROR: Failed to setup TeraChem.") - sys.exit(1) -else: - printf(" ERROR: Status on tc_setup function is not recognized!") - sys.exit(1) - -# Set QM region coordinates -qmcoords = [-4.4798000, -2.8400000, 4.2456000, - -4.8525000, -3.7649000, 4.3951000, - -3.6050000, -2.7568000, 4.9264000] -for i in range(len(qmcoords)): - qmcoords[i] /= BohrToAng - -# No MM region at the moment -mmmcharges = [] - -# Compute energy and gradient -print("") -totenergy, qmgrad, mmgrad, status = tc.compute_energy_gradient(qmattypes,qmcoords,globaltreatment=0) -if (status == 0): - print(" Computed energy and gradient with success.") -elif (status == 1): - print(" ERROR: Mismatch in the variables passed to the function to compute energy and gradient!") - sys.exit(1) -elif (status == 2): - print(" ERROR: Problem to compute energy and gradient!") - sys.exit(1) -else: - printf(" ERROR: Status on tc_compute_energy_gradient function is not recognized!") - sys.exit(1) - -# Print results -print(" Results from 1st calculation (only one water molecule in the QM region)") -print("E = %16.10f Hartrees"%(totenergy)) -for i in range(len(qmattypes)): - print("QM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr"%(i+1,qmgrad[3*i], qmgrad[3*i+1], qmgrad[3*i+2])) - -# We now add an MM region -mmcoords = [-2.6793000, -2.1596000, 5.9264000, - -1.7944000, -2.5941000, 6.0208000, - -2.4543000, -1.2247000, 5.9247000, - -6.0739000, -0.8812700, 5.2104000, - -5.3910000, -1.5014000, 4.7942000, - -5.4189000, -0.3240900, 5.9375000, - -4.0898000, -5.6279000, 2.9956000, - -4.6091000, -5.6876000, 2.2341000, - -4.1166000, -6.5262000, 3.2888000, - -2.3448000, -2.6425000, 1.8190000, - -2.7846000, -3.1506000, 2.6164000, - -1.5986000, -3.2938000, 1.7252000, - -4.6456000, -4.4223000, 7.4705000, - -3.6650000, -4.5356000, 7.1235000, - -4.9759000, -3.5580000, 7.3041000 ] -for i in range(len(mmcoords)): - mmcoords[i] /= BohrToAng -mmcharges = [ -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417 ] - -# Compute energy and gradient -print("") -totenergy, qmgrad, mmgrad, status = tc.compute_energy_gradient(qmattypes,qmcoords,mmcoords,mmcharges,globaltreatment=0) -if (status == 0): - print(" Computed energy and gradient with success.") -elif (status == 1): - print(" ERROR: Mismatch in the variables passed to the function to compute energy and gradient!") - sys.exit(1) -elif (status == 2): - print(" ERROR: Problem to compute energy and gradient!") - sys.exit(1) -else: - print(" ERROR: Status on tc_compute_energy_gradient function is not recognized!") - sys.exit(1) - -# Print results -print(" Results from 2nd calculation (one water molecule in the QM region and five in the MM region)") -print("E = %16.10f Hartrees"%(totenergy)) -for i in range(len(qmattypes)): - print("QM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr"%(i+1,qmgrad[3*i], qmgrad[3*i+1], qmgrad[3*i+2])) -for i in range(len(mmcharges)): - print("MM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr"%(i+1,mmgrad[3*i], mmgrad[3*i+1], mmgrad[3*i+2])) - -# Compute energy and gradient -print("") -totenergy, qmgrad, mmgrad, status = tc.compute_energy_gradient(qmattypes,qmcoords,mmcoords,mmcharges,globaltreatment=0) -if (status == 0): - print(" Computed energy and gradient with success.") -elif (status == 1): - print(" ERROR: Mismatch in the variables passed to the function to compute energy and gradient!") - sys.exit(1) -elif (status == 2): - print(" ERROR: Problem to compute energy and gradient!") - sys.exit(1) -else: - print(" ERROR: Status on tc_compute_energy_gradient function is not recognized!") - sys.exit(1) - -# Print results -print(" Results from 3rd calculation (just repeating the 2nd calculation)") -print("E = %16.10f Hartrees"%(totenergy)) -for i in range(len(qmattypes)): - print("QM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr"%(i+1,qmgrad[3*i], qmgrad[3*i+1], qmgrad[3*i+2])) -for i in range(len(mmcharges)): - print("MM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr"%(i+1,mmgrad[3*i], mmgrad[3*i+1], mmgrad[3*i+2])) - -# Change coordinates of the QM region -qmcoords = [-4.4748000, -2.8700000, 4.5456000, - -4.8525000, -3.7649000, 4.3951000, - -3.6050000, -2.7568000, 4.9264000 ] -for i in range(len(qmcoords)): - qmcoords[i] /= BohrToAng - -# Compute energy and gradient -print("") -totenergy, qmgrad, mmgrad, status = tc.compute_energy_gradient(qmattypes,qmcoords,mmcoords,mmcharges,globaltreatment=0) -if (status == 0): - print(" Computed energy and gradient with success.") -elif (status == 1): - print(" ERROR: Mismatch in the variables passed to the function to compute energy and gradient!") - sys.exit(1) -elif (status == 2): - print(" ERROR: Problem to compute energy and gradient!") - sys.exit(1) -else: - print(" ERROR: Status on tc_compute_energy_gradient function is not recognized!") - sys.exit(1) - -# Print results -print(" Results from 4th calculation (changed coordinates of the QM region)") -print("E = %16.10f Hartrees"%(totenergy)) -for i in range(len(qmattypes)): - print("QM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr"%(i+1,qmgrad[3*i], qmgrad[3*i+1], qmgrad[3*i+2])) -for i in range(len(mmcharges)): - print("MM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr"%(i+1,mmgrad[3*i], mmgrad[3*i+1], mmgrad[3*i+2])) - -# Move one water molecule from the MM region to the QM region -qmattypes = ["O","H","H","O","H","H"] -qmcoords = [-4.4798000, -2.8400000, 4.2456000, - -4.8525000, -3.7649000, 4.3951000, - -3.6050000, -2.7568000, 4.9264000, - -2.6793000, -2.1596000, 5.9264000, - -1.7944000, -2.5941000, 6.0208000, - -2.4543000, -1.2247000, 5.9247000 ] -for i in range(len(qmcoords)): - qmcoords[i] /= BohrToAng -mmcoords = [-6.0739000, -0.8812700, 5.2104000, - -5.3910000, -1.5014000, 4.7942000, - -5.4189000, -0.3240900, 5.9375000, - -4.0898000, -5.6279000, 2.9956000, - -4.6091000, -5.6876000, 2.2341000, - -4.1166000, -6.5262000, 3.2888000, - -2.3448000, -2.6425000, 1.8190000, - -2.7846000, -3.1506000, 2.6164000, - -1.5986000, -3.2938000, 1.7252000, - -4.6456000, -4.4223000, 7.4705000, - -3.6650000, -4.5356000, 7.1235000, - -4.9759000, -3.5580000, 7.3041000 ] -for i in range(len(mmcoords)): - mmcoords[i] /= BohrToAng -mmcharges = [ -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417, - -0.834, - 0.417, - 0.417 ] - -# Compute energy and gradient -print("") -totenergy, qmgrad, mmgrad, status = tc.compute_energy_gradient(qmattypes,qmcoords,mmcoords,mmcharges,globaltreatment=0) -if (status == 0): - print(" Computed energy and gradient with success.") -elif (status == 1): - print(" ERROR: Mismatch in the variables passed to the function to compute energy and gradient!") - sys.exit(1) -elif (status == 2): - print(" ERROR: Problem to compute energy and gradient!") - sys.exit(1) -else: - print(" ERROR: Status on tc_compute_energy_gradient function is not recognized!") - sys.exit(1) - -# Print results -print(" Results from 5th calculation (moved one molecule from the MM to the QM region)") -print("E = %16.10f Hartrees"%(totenergy)) -for i in range(len(qmattypes)): - print("QM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr"%(i+1,qmgrad[3*i], qmgrad[3*i+1], qmgrad[3*i+2])) -for i in range(len(mmcharges)): - print("MM Grad(%3d,:) = %16.10f%16.10f%16.10f Hartree/Bohr"%(i+1,mmgrad[3*i], mmgrad[3*i+1], mmgrad[3*i+2])) - -# Finalizes variables on the TeraChem side -tc.finalize() - -# Delete variables that have been allocated -del qmattypes, qmcoords, qmgrad, mmcoords, mmcharges, mmgrad \ No newline at end of file diff --git AmberTools/src/tcpb-cpp/configure AmberTools/src/tcpb-cpp/configure index e830e1b..ada8a1d 100755 --- AmberTools/src/tcpb-cpp/configure +++ AmberTools/src/tcpb-cpp/configure @@ -55,7 +55,6 @@ if arg[0].lower() in ('gnu', 'gcc'): cpp = 'g++' f90 = 'gfortran' ldflags = ['-lprotobuf'] - tests_ldflags = ['-lprotobuf','-ltcpb'] cppflags = ['-fPIC -std=c++11 -pthread -Wall'] f90flags = ['-fPIC', '-Wall'] @@ -79,7 +78,6 @@ elif arg[0].lower() == 'clang': cpp = 'clang++' f90 = 'gfortran' ldflags = ['-lprotobuf'] - tests_ldflags = ['-lprotobuf','-ltcpb'] cppflags = ['-fPIC -std=c++11 -pthread -Wall'] f90flags = ['-fPIC', '-Wall'] @@ -103,7 +101,6 @@ else: cpp = 'icpc' f90 = 'ifort' ldflags = ['-lprotobuf'] - tests_ldflags = ['-lprotobuf','-ltcpb'] cppflags = ['-fPIC -std=c++11 -pthread -Wall'] f90flags = ['-fPIC', '-warn', 'all'] @@ -121,7 +118,7 @@ else: f90flags.extend(['-g', '-debug']) ldflags.extend(['-g', '-debug']) -confighopts = dict(cpp=cpp, f90=f90, ldflags=' '.join(ldflags), tests_ldflags=' '.join(tests_ldflags), +confighopts = dict(cpp=cpp, f90=f90, ldflags=' '.join(ldflags), cppflags=' '.join(cppflags), f90flags=' '.join(f90flags), confline=' '.join(sys.argv), prefix=opt.prefix) f.write("""# configured with [[ %(confline)s ]] @@ -135,11 +132,9 @@ PROTOC = protoc FFLAGS = %(f90flags)s TCPB_CXXFLAGS = %(cppflags)s TCPB_LDFLAGS = %(ldflags)s -TESTS_LDFLAGS = %(tests_ldflags)s # Where program gets installed LIBDIR = %(prefix)s/lib INCDIR = %(prefix)s/include -TESTDIR = %(prefix)s/tests """ % confighopts) f.close() diff --git AmberTools/src/tcpb-cpp/docs/Doxyfile AmberTools/src/tcpb-cpp/docs/Doxyfile deleted file mode 100644 index 91d24d7..0000000 --- AmberTools/src/tcpb-cpp/docs/Doxyfile +++ /dev/null @@ -1,2537 +0,0 @@ -# Doxyfile 1.8.16 - -# This file describes the settings to be used by the documentation system -# doxygen (www.doxygen.org) for a project. -# -# All text after a double hash (##) is considered a comment and is placed in -# front of the TAG it is preceding. -# -# All text after a single hash (#) is considered a comment and will be ignored. -# The format is: -# TAG = value [value, ...] -# For lists, items can also be appended using: -# TAG += value [value, ...] -# Values that contain spaces should be placed between quotes (\" \"). - -#--------------------------------------------------------------------------- -# Project related configuration options -#--------------------------------------------------------------------------- - -# This tag specifies the encoding used for all characters in the configuration -# file that follow. The default is UTF-8 which is also the encoding used for all -# text before the first occurrence of this tag. Doxygen uses libiconv (or the -# iconv built into libc) for the transcoding. See -# https://www.gnu.org/software/libiconv/ for the list of possible encodings. -# The default value is: UTF-8. - -DOXYFILE_ENCODING = UTF-8 - -# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by -# double-quotes, unless you are using Doxywizard) that should identify the -# project for which the documentation is generated. This name is used in the -# title of most generated pages and in a few other places. -# The default value is: My Project. - -PROJECT_NAME = "C++ TeraChem Protocol Buffer Interfaces" - -# The PROJECT_NUMBER tag can be used to enter a project or revision number. This -# could be handy for archiving the generated documentation or if some version -# control system is used. - -PROJECT_NUMBER = - -# Using the PROJECT_BRIEF tag one can provide an optional one line description -# for a project that appears at the top of each page and should give viewer a -# quick idea about the purpose of the project. Keep the description short. - -PROJECT_BRIEF = "C++ interfaces for TeraChem Protocol Buffer clients and servers" - -# With the PROJECT_LOGO tag one can specify a logo or an icon that is included -# in the documentation. The maximum height of the logo should not exceed 55 -# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy -# the logo to the output directory. - -PROJECT_LOGO = - -# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path -# into which the generated documentation will be written. If a relative path is -# entered, it will be relative to the location where doxygen was started. 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If set to NO, these declarations will be -# included in the documentation. -# The default value is: NO. - -HIDE_FRIEND_COMPOUNDS = NO - -# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any -# documentation blocks found inside the body of a function. If set to NO, these -# blocks will be appended to the function's detailed documentation block. -# The default value is: NO. - -HIDE_IN_BODY_DOCS = NO - -# The INTERNAL_DOCS tag determines if documentation that is typed after a -# \internal command is included. If the tag is set to NO then the documentation -# will be excluded. Set it to YES to include the internal documentation. -# The default value is: NO. - -INTERNAL_DOCS = NO - -# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file -# names in lower-case letters. If set to YES, upper-case letters are also -# allowed. This is useful if you have classes or files whose names only differ -# in case and if your file system supports case sensitive file names. Windows -# (including Cygwin) ands Mac users are advised to set this option to NO. -# The default value is: system dependent. - -CASE_SENSE_NAMES = NO - -# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with -# their full class and namespace scopes in the documentation. If set to YES, the -# scope will be hidden. -# The default value is: NO. - -HIDE_SCOPE_NAMES = NO - -# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will -# append additional text to a page's title, such as Class Reference. If set to -# YES the compound reference will be hidden. -# The default value is: NO. - -HIDE_COMPOUND_REFERENCE= NO - -# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of -# the files that are included by a file in the documentation of that file. -# The default value is: YES. - -SHOW_INCLUDE_FILES = YES - -# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each -# grouped member an include statement to the documentation, telling the reader -# which file to include in order to use the member. -# The default value is: NO. - -SHOW_GROUPED_MEMB_INC = NO - -# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include -# files with double quotes in the documentation rather than with sharp brackets. -# The default value is: NO. - -FORCE_LOCAL_INCLUDES = NO - -# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the -# documentation for inline members. -# The default value is: YES. - -INLINE_INFO = YES - -# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the -# (detailed) documentation of file and class members alphabetically by member -# name. If set to NO, the members will appear in declaration order. -# The default value is: YES. - -SORT_MEMBER_DOCS = YES - -# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief -# descriptions of file, namespace and class members alphabetically by member -# name. If set to NO, the members will appear in declaration order. Note that -# this will also influence the order of the classes in the class list. -# The default value is: NO. - -SORT_BRIEF_DOCS = NO - -# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the -# (brief and detailed) documentation of class members so that constructors and -# destructors are listed first. If set to NO the constructors will appear in the -# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. -# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief -# member documentation. -# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting -# detailed member documentation. -# The default value is: NO. - -SORT_MEMBERS_CTORS_1ST = NO - -# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy -# of group names into alphabetical order. If set to NO the group names will -# appear in their defined order. -# The default value is: NO. - -SORT_GROUP_NAMES = NO - -# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by -# fully-qualified names, including namespaces. If set to NO, the class list will -# be sorted only by class name, not including the namespace part. -# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. -# Note: This option applies only to the class list, not to the alphabetical -# list. -# The default value is: NO. - -SORT_BY_SCOPE_NAME = NO - -# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper -# type resolution of all parameters of a function it will reject a match between -# the prototype and the implementation of a member function even if there is -# only one candidate or it is obvious which candidate to choose by doing a -# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still -# accept a match between prototype and implementation in such cases. -# The default value is: NO. - -STRICT_PROTO_MATCHING = NO - -# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo -# list. This list is created by putting \todo commands in the documentation. -# The default value is: YES. - -GENERATE_TODOLIST = YES - -# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test -# list. This list is created by putting \test commands in the documentation. -# The default value is: YES. - -GENERATE_TESTLIST = YES - -# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug -# list. This list is created by putting \bug commands in the documentation. -# The default value is: YES. - -GENERATE_BUGLIST = YES - -# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) -# the deprecated list. This list is created by putting \deprecated commands in -# the documentation. -# The default value is: YES. - -GENERATE_DEPRECATEDLIST= YES - -# The ENABLED_SECTIONS tag can be used to enable conditional documentation -# sections, marked by \if ... \endif and \cond -# ... \endcond blocks. - -ENABLED_SECTIONS = - -# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the -# initial value of a variable or macro / define can have for it to appear in the -# documentation. If the initializer consists of more lines than specified here -# it will be hidden. Use a value of 0 to hide initializers completely. The -# appearance of the value of individual variables and macros / defines can be -# controlled using \showinitializer or \hideinitializer command in the -# documentation regardless of this setting. -# Minimum value: 0, maximum value: 10000, default value: 30. - -MAX_INITIALIZER_LINES = 30 - -# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at -# the bottom of the documentation of classes and structs. If set to YES, the -# list will mention the files that were used to generate the documentation. -# The default value is: YES. - -SHOW_USED_FILES = YES - -# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This -# will remove the Files entry from the Quick Index and from the Folder Tree View -# (if specified). -# The default value is: YES. - -SHOW_FILES = YES - -# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces -# page. This will remove the Namespaces entry from the Quick Index and from the -# Folder Tree View (if specified). -# The default value is: YES. - -SHOW_NAMESPACES = YES - -# The FILE_VERSION_FILTER tag can be used to specify a program or script that -# doxygen should invoke to get the current version for each file (typically from -# the version control system). Doxygen will invoke the program by executing (via -# popen()) the command command input-file, where command is the value of the -# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided -# by doxygen. Whatever the program writes to standard output is used as the file -# version. For an example see the documentation. - -FILE_VERSION_FILTER = - -# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed -# by doxygen. The layout file controls the global structure of the generated -# output files in an output format independent way. To create the layout file -# that represents doxygen's defaults, run doxygen with the -l option. You can -# optionally specify a file name after the option, if omitted DoxygenLayout.xml -# will be used as the name of the layout file. -# -# Note that if you run doxygen from a directory containing a file called -# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE -# tag is left empty. - -LAYOUT_FILE = - -# The CITE_BIB_FILES tag can be used to specify one or more bib files containing -# the reference definitions. This must be a list of .bib files. The .bib -# extension is automatically appended if omitted. This requires the bibtex tool -# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info. -# For LaTeX the style of the bibliography can be controlled using -# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the -# search path. See also \cite for info how to create references. - -CITE_BIB_FILES = - -#--------------------------------------------------------------------------- -# Configuration options related to warning and progress messages -#--------------------------------------------------------------------------- - -# The QUIET tag can be used to turn on/off the messages that are generated to -# standard output by doxygen. If QUIET is set to YES this implies that the -# messages are off. -# The default value is: NO. - -QUIET = NO - -# The WARNINGS tag can be used to turn on/off the warning messages that are -# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES -# this implies that the warnings are on. -# -# Tip: Turn warnings on while writing the documentation. -# The default value is: YES. - -WARNINGS = YES - -# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate -# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag -# will automatically be disabled. -# The default value is: YES. - -WARN_IF_UNDOCUMENTED = YES - -# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for -# potential errors in the documentation, such as not documenting some parameters -# in a documented function, or documenting parameters that don't exist or using -# markup commands wrongly. -# The default value is: YES. - -WARN_IF_DOC_ERROR = YES - -# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that -# are documented, but have no documentation for their parameters or return -# value. If set to NO, doxygen will only warn about wrong or incomplete -# parameter documentation, but not about the absence of documentation. If -# EXTRACT_ALL is set to YES then this flag will automatically be disabled. -# The default value is: NO. - -WARN_NO_PARAMDOC = NO - -# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when -# a warning is encountered. -# The default value is: NO. - -WARN_AS_ERROR = NO - -# The WARN_FORMAT tag determines the format of the warning messages that doxygen -# can produce. The string should contain the $file, $line, and $text tags, which -# will be replaced by the file and line number from which the warning originated -# and the warning text. Optionally the format may contain $version, which will -# be replaced by the version of the file (if it could be obtained via -# FILE_VERSION_FILTER) -# The default value is: $file:$line: $text. - -WARN_FORMAT = "$file:$line: $text" - -# The WARN_LOGFILE tag can be used to specify a file to which warning and error -# messages should be written. If left blank the output is written to standard -# error (stderr). - -WARN_LOGFILE = - -#--------------------------------------------------------------------------- -# Configuration options related to the input files -#--------------------------------------------------------------------------- - -# The INPUT tag is used to specify the files and/or directories that contain -# documented source files. You may enter file names like myfile.cpp or -# directories like /usr/src/myproject. Separate the files or directories with -# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING -# Note: If this tag is empty the current directory is searched. - -INPUT = ../src/ - -# This tag can be used to specify the character encoding of the source files -# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses -# libiconv (or the iconv built into libc) for the transcoding. See the libiconv -# documentation (see: https://www.gnu.org/software/libiconv/) for the list of -# possible encodings. -# The default value is: UTF-8. - -INPUT_ENCODING = UTF-8 - -# If the value of the INPUT tag contains directories, you can use the -# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and -# *.h) to filter out the source-files in the directories. -# -# Note that for custom extensions or not directly supported extensions you also -# need to set EXTENSION_MAPPING for the extension otherwise the files are not -# read by doxygen. -# -# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, -# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, -# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, -# *.m, *.markdown, *.md, *.mm, *.dox, *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, -# *.f, *.for, *.tcl, *.vhd, *.vhdl, *.ucf, *.qsf and *.ice. - -FILE_PATTERNS = *.c \ - *.cc \ - *.cxx \ - *.cpp \ - *.c++ \ - *.java \ - *.ii \ - *.ixx \ - *.ipp \ - *.i++ \ - *.inl \ - *.idl \ - *.ddl \ - *.odl \ - *.h \ - *.hh \ - *.hxx \ - *.hpp \ - *.h++ \ - *.cs \ - *.d \ - *.php \ - *.php4 \ - *.php5 \ - *.phtml \ - *.inc \ - *.m \ - *.markdown \ - *.md \ - *.mm \ - *.dox \ - *.py \ - *.pyw \ - *.f90 \ - *.f95 \ - *.f03 \ - *.f08 \ - *.f \ - *.for \ - *.tcl \ - *.vhd \ - *.vhdl \ - *.ucf \ - *.qsf - -# The RECURSIVE tag can be used to specify whether or not subdirectories should -# be searched for input files as well. -# The default value is: NO. - -RECURSIVE = YES - -# The EXCLUDE tag can be used to specify files and/or directories that should be -# excluded from the INPUT source files. This way you can easily exclude a -# subdirectory from a directory tree whose root is specified with the INPUT tag. -# -# Note that relative paths are relative to the directory from which doxygen is -# run. - -EXCLUDE = ../src/terachem_server.* - -# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or -# directories that are symbolic links (a Unix file system feature) are excluded -# from the input. -# The default value is: NO. - -EXCLUDE_SYMLINKS = NO - -# If the value of the INPUT tag contains directories, you can use the -# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude -# certain files from those directories. -# -# Note that the wildcards are matched against the file with absolute path, so to -# exclude all test directories for example use the pattern */test/* - -EXCLUDE_PATTERNS = - -# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names -# (namespaces, classes, functions, etc.) that should be excluded from the -# output. The symbol name can be a fully qualified name, a word, or if the -# wildcard * is used, a substring. Examples: ANamespace, AClass, -# AClass::ANamespace, ANamespace::*Test -# -# Note that the wildcards are matched against the file with absolute path, so to -# exclude all test directories use the pattern */test/* - -EXCLUDE_SYMBOLS = - -# The EXAMPLE_PATH tag can be used to specify one or more files or directories -# that contain example code fragments that are included (see the \include -# command). - -EXAMPLE_PATH = - -# If the value of the EXAMPLE_PATH tag contains directories, you can use the -# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and -# *.h) to filter out the source-files in the directories. If left blank all -# files are included. - -EXAMPLE_PATTERNS = * - -# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be -# searched for input files to be used with the \include or \dontinclude commands -# irrespective of the value of the RECURSIVE tag. -# The default value is: NO. - -EXAMPLE_RECURSIVE = NO - -# The IMAGE_PATH tag can be used to specify one or more files or directories -# that contain images that are to be included in the documentation (see the -# \image command). - -IMAGE_PATH = - -# The INPUT_FILTER tag can be used to specify a program that doxygen should -# invoke to filter for each input file. Doxygen will invoke the filter program -# by executing (via popen()) the command: -# -# -# -# where is the value of the INPUT_FILTER tag, and is the -# name of an input file. Doxygen will then use the output that the filter -# program writes to standard output. If FILTER_PATTERNS is specified, this tag -# will be ignored. -# -# Note that the filter must not add or remove lines; it is applied before the -# code is scanned, but not when the output code is generated. If lines are added -# or removed, the anchors will not be placed correctly. -# -# Note that for custom extensions or not directly supported extensions you also -# need to set EXTENSION_MAPPING for the extension otherwise the files are not -# properly processed by doxygen. - -INPUT_FILTER = - -# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern -# basis. Doxygen will compare the file name with each pattern and apply the -# filter if there is a match. The filters are a list of the form: pattern=filter -# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how -# filters are used. If the FILTER_PATTERNS tag is empty or if none of the -# patterns match the file name, INPUT_FILTER is applied. -# -# Note that for custom extensions or not directly supported extensions you also -# need to set EXTENSION_MAPPING for the extension otherwise the files are not -# properly processed by doxygen. - -FILTER_PATTERNS = - -# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using -# INPUT_FILTER) will also be used to filter the input files that are used for -# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). -# The default value is: NO. - -FILTER_SOURCE_FILES = NO - -# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file -# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and -# it is also possible to disable source filtering for a specific pattern using -# *.ext= (so without naming a filter). -# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. - -FILTER_SOURCE_PATTERNS = - -# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that -# is part of the input, its contents will be placed on the main page -# (index.html). This can be useful if you have a project on for instance GitHub -# and want to reuse the introduction page also for the doxygen output. - -USE_MDFILE_AS_MAINPAGE = - -#--------------------------------------------------------------------------- -# Configuration options related to source browsing -#--------------------------------------------------------------------------- - -# If the SOURCE_BROWSER tag is set to YES then a list of source files will be -# generated. Documented entities will be cross-referenced with these sources. -# -# Note: To get rid of all source code in the generated output, make sure that -# also VERBATIM_HEADERS is set to NO. -# The default value is: NO. - -SOURCE_BROWSER = NO - -# Setting the INLINE_SOURCES tag to YES will include the body of functions, -# classes and enums directly into the documentation. -# The default value is: NO. - -INLINE_SOURCES = NO - -# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any -# special comment blocks from generated source code fragments. Normal C, C++ and -# Fortran comments will always remain visible. -# The default value is: YES. - -STRIP_CODE_COMMENTS = YES - -# If the REFERENCED_BY_RELATION tag is set to YES then for each documented -# entity all documented functions referencing it will be listed. -# The default value is: NO. - -REFERENCED_BY_RELATION = NO - -# If the REFERENCES_RELATION tag is set to YES then for each documented function -# all documented entities called/used by that function will be listed. -# The default value is: NO. - -REFERENCES_RELATION = NO - -# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set -# to YES then the hyperlinks from functions in REFERENCES_RELATION and -# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will -# link to the documentation. -# The default value is: YES. - -REFERENCES_LINK_SOURCE = YES - -# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the -# source code will show a tooltip with additional information such as prototype, -# brief description and links to the definition and documentation. Since this -# will make the HTML file larger and loading of large files a bit slower, you -# can opt to disable this feature. -# The default value is: YES. -# This tag requires that the tag SOURCE_BROWSER is set to YES. - -SOURCE_TOOLTIPS = YES - -# If the USE_HTAGS tag is set to YES then the references to source code will -# point to the HTML generated by the htags(1) tool instead of doxygen built-in -# source browser. The htags tool is part of GNU's global source tagging system -# (see https://www.gnu.org/software/global/global.html). You will need version -# 4.8.6 or higher. -# -# To use it do the following: -# - Install the latest version of global -# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file -# - Make sure the INPUT points to the root of the source tree -# - Run doxygen as normal -# -# Doxygen will invoke htags (and that will in turn invoke gtags), so these -# tools must be available from the command line (i.e. in the search path). -# -# The result: instead of the source browser generated by doxygen, the links to -# source code will now point to the output of htags. -# The default value is: NO. -# This tag requires that the tag SOURCE_BROWSER is set to YES. - -USE_HTAGS = NO - -# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a -# verbatim copy of the header file for each class for which an include is -# specified. Set to NO to disable this. -# See also: Section \class. -# The default value is: YES. - -VERBATIM_HEADERS = YES - -#--------------------------------------------------------------------------- -# Configuration options related to the alphabetical class index -#--------------------------------------------------------------------------- - -# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all -# compounds will be generated. Enable this if the project contains a lot of -# classes, structs, unions or interfaces. -# The default value is: YES. - -ALPHABETICAL_INDEX = YES - -# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in -# which the alphabetical index list will be split. -# Minimum value: 1, maximum value: 20, default value: 5. -# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. - -COLS_IN_ALPHA_INDEX = 5 - -# In case all classes in a project start with a common prefix, all classes will -# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag -# can be used to specify a prefix (or a list of prefixes) that should be ignored -# while generating the index headers. -# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. - -IGNORE_PREFIX = - -#--------------------------------------------------------------------------- -# Configuration options related to the HTML output -#--------------------------------------------------------------------------- - -# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output -# The default value is: YES. - -GENERATE_HTML = YES - -# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a -# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of -# it. -# The default directory is: html. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_OUTPUT = html - -# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each -# generated HTML page (for example: .htm, .php, .asp). -# The default value is: .html. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_FILE_EXTENSION = .html - -# The HTML_HEADER tag can be used to specify a user-defined HTML header file for -# each generated HTML page. If the tag is left blank doxygen will generate a -# standard header. -# -# To get valid HTML the header file that includes any scripts and style sheets -# that doxygen needs, which is dependent on the configuration options used (e.g. -# the setting GENERATE_TREEVIEW). It is highly recommended to start with a -# default header using -# doxygen -w html new_header.html new_footer.html new_stylesheet.css -# YourConfigFile -# and then modify the file new_header.html. See also section "Doxygen usage" -# for information on how to generate the default header that doxygen normally -# uses. -# Note: The header is subject to change so you typically have to regenerate the -# default header when upgrading to a newer version of doxygen. For a description -# of the possible markers and block names see the documentation. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_HEADER = - -# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each -# generated HTML page. If the tag is left blank doxygen will generate a standard -# footer. See HTML_HEADER for more information on how to generate a default -# footer and what special commands can be used inside the footer. See also -# section "Doxygen usage" for information on how to generate the default footer -# that doxygen normally uses. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_FOOTER = - -# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style -# sheet that is used by each HTML page. It can be used to fine-tune the look of -# the HTML output. If left blank doxygen will generate a default style sheet. -# See also section "Doxygen usage" for information on how to generate the style -# sheet that doxygen normally uses. -# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as -# it is more robust and this tag (HTML_STYLESHEET) will in the future become -# obsolete. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_STYLESHEET = - -# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined -# cascading style sheets that are included after the standard style sheets -# created by doxygen. Using this option one can overrule certain style aspects. -# This is preferred over using HTML_STYLESHEET since it does not replace the -# standard style sheet and is therefore more robust against future updates. -# Doxygen will copy the style sheet files to the output directory. -# Note: The order of the extra style sheet files is of importance (e.g. the last -# style sheet in the list overrules the setting of the previous ones in the -# list). For an example see the documentation. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_EXTRA_STYLESHEET = - -# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or -# other source files which should be copied to the HTML output directory. Note -# that these files will be copied to the base HTML output directory. Use the -# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these -# files. In the HTML_STYLESHEET file, use the file name only. Also note that the -# files will be copied as-is; there are no commands or markers available. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_EXTRA_FILES = - -# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen -# will adjust the colors in the style sheet and background images according to -# this color. Hue is specified as an angle on a colorwheel, see -# https://en.wikipedia.org/wiki/Hue for more information. For instance the value -# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 -# purple, and 360 is red again. -# Minimum value: 0, maximum value: 359, default value: 220. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_COLORSTYLE_HUE = 220 - -# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors -# in the HTML output. For a value of 0 the output will use grayscales only. A -# value of 255 will produce the most vivid colors. -# Minimum value: 0, maximum value: 255, default value: 100. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_COLORSTYLE_SAT = 100 - -# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the -# luminance component of the colors in the HTML output. Values below 100 -# gradually make the output lighter, whereas values above 100 make the output -# darker. The value divided by 100 is the actual gamma applied, so 80 represents -# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not -# change the gamma. -# Minimum value: 40, maximum value: 240, default value: 80. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_COLORSTYLE_GAMMA = 80 - -# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML -# page will contain the date and time when the page was generated. Setting this -# to YES can help to show when doxygen was last run and thus if the -# documentation is up to date. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_TIMESTAMP = NO - -# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML -# documentation will contain a main index with vertical navigation menus that -# are dynamically created via Javascript. If disabled, the navigation index will -# consists of multiple levels of tabs that are statically embedded in every HTML -# page. Disable this option to support browsers that do not have Javascript, -# like the Qt help browser. -# The default value is: YES. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_DYNAMIC_MENUS = YES - -# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML -# documentation will contain sections that can be hidden and shown after the -# page has loaded. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_DYNAMIC_SECTIONS = NO - -# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries -# shown in the various tree structured indices initially; the user can expand -# and collapse entries dynamically later on. Doxygen will expand the tree to -# such a level that at most the specified number of entries are visible (unless -# a fully collapsed tree already exceeds this amount). So setting the number of -# entries 1 will produce a full collapsed tree by default. 0 is a special value -# representing an infinite number of entries and will result in a full expanded -# tree by default. -# Minimum value: 0, maximum value: 9999, default value: 100. -# This tag requires that the tag GENERATE_HTML is set to YES. - -HTML_INDEX_NUM_ENTRIES = 100 - -# If the GENERATE_DOCSET tag is set to YES, additional index files will be -# generated that can be used as input for Apple's Xcode 3 integrated development -# environment (see: https://developer.apple.com/xcode/), introduced with OSX -# 10.5 (Leopard). To create a documentation set, doxygen will generate a -# Makefile in the HTML output directory. Running make will produce the docset in -# that directory and running make install will install the docset in -# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at -# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy -# genXcode/_index.html for more information. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -GENERATE_DOCSET = NO - -# This tag determines the name of the docset feed. A documentation feed provides -# an umbrella under which multiple documentation sets from a single provider -# (such as a company or product suite) can be grouped. -# The default value is: Doxygen generated docs. -# This tag requires that the tag GENERATE_DOCSET is set to YES. - -DOCSET_FEEDNAME = "Doxygen generated docs" - -# This tag specifies a string that should uniquely identify the documentation -# set bundle. This should be a reverse domain-name style string, e.g. -# com.mycompany.MyDocSet. Doxygen will append .docset to the name. -# The default value is: org.doxygen.Project. -# This tag requires that the tag GENERATE_DOCSET is set to YES. - -DOCSET_BUNDLE_ID = org.doxygen.Project - -# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify -# the documentation publisher. This should be a reverse domain-name style -# string, e.g. com.mycompany.MyDocSet.documentation. -# The default value is: org.doxygen.Publisher. -# This tag requires that the tag GENERATE_DOCSET is set to YES. - -DOCSET_PUBLISHER_ID = org.doxygen.Publisher - -# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. -# The default value is: Publisher. -# This tag requires that the tag GENERATE_DOCSET is set to YES. - -DOCSET_PUBLISHER_NAME = Publisher - -# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three -# additional HTML index files: index.hhp, index.hhc, and index.hhk. The -# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop -# (see: https://www.microsoft.com/en-us/download/details.aspx?id=21138) on -# Windows. -# -# The HTML Help Workshop contains a compiler that can convert all HTML output -# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML -# files are now used as the Windows 98 help format, and will replace the old -# Windows help format (.hlp) on all Windows platforms in the future. Compressed -# HTML files also contain an index, a table of contents, and you can search for -# words in the documentation. The HTML workshop also contains a viewer for -# compressed HTML files. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -GENERATE_HTMLHELP = NO - -# The CHM_FILE tag can be used to specify the file name of the resulting .chm -# file. You can add a path in front of the file if the result should not be -# written to the html output directory. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -CHM_FILE = - -# The HHC_LOCATION tag can be used to specify the location (absolute path -# including file name) of the HTML help compiler (hhc.exe). If non-empty, -# doxygen will try to run the HTML help compiler on the generated index.hhp. -# The file has to be specified with full path. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -HHC_LOCATION = - -# The GENERATE_CHI flag controls if a separate .chi index file is generated -# (YES) or that it should be included in the master .chm file (NO). -# The default value is: NO. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -GENERATE_CHI = NO - -# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) -# and project file content. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -CHM_INDEX_ENCODING = - -# The BINARY_TOC flag controls whether a binary table of contents is generated -# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it -# enables the Previous and Next buttons. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -BINARY_TOC = NO - -# The TOC_EXPAND flag can be set to YES to add extra items for group members to -# the table of contents of the HTML help documentation and to the tree view. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTMLHELP is set to YES. - -TOC_EXPAND = NO - -# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and -# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that -# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help -# (.qch) of the generated HTML documentation. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -GENERATE_QHP = NO - -# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify -# the file name of the resulting .qch file. The path specified is relative to -# the HTML output folder. -# This tag requires that the tag GENERATE_QHP is set to YES. - -QCH_FILE = - -# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help -# Project output. For more information please see Qt Help Project / Namespace -# (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace). -# The default value is: org.doxygen.Project. -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHP_NAMESPACE = org.doxygen.Project - -# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt -# Help Project output. For more information please see Qt Help Project / Virtual -# Folders (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual- -# folders). -# The default value is: doc. -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHP_VIRTUAL_FOLDER = doc - -# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom -# filter to add. For more information please see Qt Help Project / Custom -# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom- -# filters). -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHP_CUST_FILTER_NAME = - -# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the -# custom filter to add. For more information please see Qt Help Project / Custom -# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom- -# filters). -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHP_CUST_FILTER_ATTRS = - -# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this -# project's filter section matches. Qt Help Project / Filter Attributes (see: -# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes). -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHP_SECT_FILTER_ATTRS = - -# The QHG_LOCATION tag can be used to specify the location of Qt's -# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the -# generated .qhp file. -# This tag requires that the tag GENERATE_QHP is set to YES. - -QHG_LOCATION = - -# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be -# generated, together with the HTML files, they form an Eclipse help plugin. To -# install this plugin and make it available under the help contents menu in -# Eclipse, the contents of the directory containing the HTML and XML files needs -# to be copied into the plugins directory of eclipse. The name of the directory -# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. -# After copying Eclipse needs to be restarted before the help appears. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -GENERATE_ECLIPSEHELP = NO - -# A unique identifier for the Eclipse help plugin. When installing the plugin -# the directory name containing the HTML and XML files should also have this -# name. Each documentation set should have its own identifier. -# The default value is: org.doxygen.Project. -# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. - -ECLIPSE_DOC_ID = org.doxygen.Project - -# If you want full control over the layout of the generated HTML pages it might -# be necessary to disable the index and replace it with your own. The -# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top -# of each HTML page. A value of NO enables the index and the value YES disables -# it. Since the tabs in the index contain the same information as the navigation -# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -DISABLE_INDEX = NO - -# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index -# structure should be generated to display hierarchical information. If the tag -# value is set to YES, a side panel will be generated containing a tree-like -# index structure (just like the one that is generated for HTML Help). For this -# to work a browser that supports JavaScript, DHTML, CSS and frames is required -# (i.e. any modern browser). Windows users are probably better off using the -# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can -# further fine-tune the look of the index. As an example, the default style -# sheet generated by doxygen has an example that shows how to put an image at -# the root of the tree instead of the PROJECT_NAME. Since the tree basically has -# the same information as the tab index, you could consider setting -# DISABLE_INDEX to YES when enabling this option. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -GENERATE_TREEVIEW = NO - -# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that -# doxygen will group on one line in the generated HTML documentation. -# -# Note that a value of 0 will completely suppress the enum values from appearing -# in the overview section. -# Minimum value: 0, maximum value: 20, default value: 4. -# This tag requires that the tag GENERATE_HTML is set to YES. - -ENUM_VALUES_PER_LINE = 4 - -# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used -# to set the initial width (in pixels) of the frame in which the tree is shown. -# Minimum value: 0, maximum value: 1500, default value: 250. -# This tag requires that the tag GENERATE_HTML is set to YES. - -TREEVIEW_WIDTH = 250 - -# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to -# external symbols imported via tag files in a separate window. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -EXT_LINKS_IN_WINDOW = NO - -# Use this tag to change the font size of LaTeX formulas included as images in -# the HTML documentation. When you change the font size after a successful -# doxygen run you need to manually remove any form_*.png images from the HTML -# output directory to force them to be regenerated. -# Minimum value: 8, maximum value: 50, default value: 10. -# This tag requires that the tag GENERATE_HTML is set to YES. - -FORMULA_FONTSIZE = 10 - -# Use the FORMULA_TRANSPARENT tag to determine whether or not the images -# generated for formulas are transparent PNGs. Transparent PNGs are not -# supported properly for IE 6.0, but are supported on all modern browsers. -# -# Note that when changing this option you need to delete any form_*.png files in -# the HTML output directory before the changes have effect. -# The default value is: YES. -# This tag requires that the tag GENERATE_HTML is set to YES. - -FORMULA_TRANSPARENT = YES - -# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see -# https://www.mathjax.org) which uses client side Javascript for the rendering -# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX -# installed or if you want to formulas look prettier in the HTML output. When -# enabled you may also need to install MathJax separately and configure the path -# to it using the MATHJAX_RELPATH option. -# The default value is: NO. -# This tag requires that the tag GENERATE_HTML is set to YES. - -USE_MATHJAX = NO - -# When MathJax is enabled you can set the default output format to be used for -# the MathJax output. See the MathJax site (see: -# http://docs.mathjax.org/en/latest/output.html) for more details. -# Possible values are: HTML-CSS (which is slower, but has the best -# compatibility), NativeMML (i.e. MathML) and SVG. -# The default value is: HTML-CSS. -# This tag requires that the tag USE_MATHJAX is set to YES. - -MATHJAX_FORMAT = HTML-CSS - -# When MathJax is enabled you need to specify the location relative to the HTML -# output directory using the MATHJAX_RELPATH option. The destination directory -# should contain the MathJax.js script. For instance, if the mathjax directory -# is located at the same level as the HTML output directory, then -# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax -# Content Delivery Network so you can quickly see the result without installing -# MathJax. However, it is strongly recommended to install a local copy of -# MathJax from https://www.mathjax.org before deployment. -# The default value is: https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/. -# This tag requires that the tag USE_MATHJAX is set to YES. - -MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest - -# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax -# extension names that should be enabled during MathJax rendering. For example -# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols -# This tag requires that the tag USE_MATHJAX is set to YES. - -MATHJAX_EXTENSIONS = - -# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces -# of code that will be used on startup of the MathJax code. See the MathJax site -# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an -# example see the documentation. -# This tag requires that the tag USE_MATHJAX is set to YES. - -MATHJAX_CODEFILE = - -# When the SEARCHENGINE tag is enabled doxygen will generate a search box for -# the HTML output. The underlying search engine uses javascript and DHTML and -# should work on any modern browser. Note that when using HTML help -# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) -# there is already a search function so this one should typically be disabled. -# For large projects the javascript based search engine can be slow, then -# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to -# search using the keyboard; to jump to the search box use + S -# (what the is depends on the OS and browser, but it is typically -# , /