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Merged
xumi1993 merged 6 commits into from
Aug 7, 2026
Merged

Update version to 2.1.1 and improve CMake configuration #39

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60f9bc9
Update project version to 2.1.1 and modify CMake configuration for ya…
xumi1993 Aug 4, 2026
6eb57d0
Refactor model field handling in rotation: enhance dataset validation…
xumi1993 Aug 5, 2026
289fb6c
Merge pull request #37 from TomoATT/main
xumi1993 Aug 5, 2026
cb977f6
Merge pull request #36 from TomoATT/devel_MX
HouseJaay Aug 6, 2026
2b3f6b8
fix typos in input_params
HouseJaay Aug 7, 2026
0dd2b1f
Merge pull request #38 from TomoATT/dev_sj
xumi1993 Aug 7, 2026
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34 changes: 24 additions & 10 deletions CMakeLists.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
cmake_minimum_required(VERSION 3.18)

project( SurfATT VERSION 2.1.0 LANGUAGES CXX Fortran)
project( SurfATT VERSION 2.1.1 LANGUAGES CXX Fortran)

include(GNUInstallDirs)

Expand Down Expand Up @@ -143,9 +143,12 @@ endif()
add_subdirectory(external_libs)

# yaml-cpp: prefer a system installation, fall back to the bundled submodule.
find_package(yaml-cpp QUIET)
if (yaml-cpp_FOUND AND NOT ${USE_EXTERNAL_LIBS})
message(STATUS "Found yaml-cpp: ${YAML_CPP_INCLUDE_DIR}")
if (NOT USE_EXTERNAL_LIBS)
find_package(yaml-cpp QUIET)
endif()

if (yaml-cpp_FOUND AND NOT USE_EXTERNAL_LIBS)
message(STATUS "Found system yaml-cpp: ${yaml-cpp_DIR}")
# Normalize to yaml-cpp::yaml-cpp to avoid deprecated target warnings.
if (NOT TARGET yaml-cpp::yaml-cpp)
if (TARGET yaml-cpp)
Expand All @@ -162,17 +165,28 @@ if (yaml-cpp_FOUND AND NOT ${USE_EXTERNAL_LIBS})
endif()
endif()
endif()
else()
message(STATUS "System yaml-cpp not found (or bundled libraries requested); using external_libs/yaml-cpp")
initialize_submodule(external_libs/yaml-cpp)
add_subdirectory(external_libs/yaml-cpp EXCLUDE_FROM_ALL)
endif()

if (NOT TARGET yaml-cpp::yaml-cpp)
message(FATAL_ERROR "yaml-cpp was found, but no usable CMake target was provided")
endif()

# ------------------------------------------------------
# find spdlog
find_package(spdlog QUIET)
if (spdlog_FOUND AND NOT ${USE_EXTERNAL_LIBS})
message(STATUS "spdlog found")
if (NOT USE_EXTERNAL_LIBS)
find_package(spdlog QUIET)
endif()

if (spdlog_FOUND AND NOT USE_EXTERNAL_LIBS)
message(STATUS "Found system spdlog: ${spdlog_DIR}")
else()
message(STATUS "spdlog not found. use source code external_libs/spdlog...")
initialize_submodule(external_libs/spdlog)
add_subdirectory(external_libs/spdlog EXCLUDE_FROM_ALL)
message(STATUS "System spdlog not found (or bundled libraries requested); using external_libs/spdlog")
initialize_submodule(external_libs/spdlog)
add_subdirectory(external_libs/spdlog EXCLUDE_FROM_ALL)
endif()

if (TARGET spdlog::spdlog_header_only)
Expand Down
20 changes: 10 additions & 10 deletions examples/01_checkerboard_azimuthal_ani/input_params.yml
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Expand Up @@ -9,7 +9,7 @@ data:
# Love-wave source-receiver files (used when wave_type[1] is true)
src_rec_file_lv_ph: OUTPUT_FILES/src_rec_file_forward_LV_PH.csv
src_rec_file_lv_gr: OUTPUT_FILES/src_rec_file_forward_LV_GR.csv
wave_type: [True, False] # [use_rayleigh, use_love] - both required for radial anisotropy
wave_type: [True, False] # [use_rayleigh, use_love]
vel_type: [True, False] # [use_phase, use_group]
weights: [1.0, 0.5] # weights for phase and group velocity

Expand All @@ -26,9 +26,9 @@ domain:
grid_method_0:
interval: [0.02, 0.02, 0.5] # interval of lon(degree), lat(degree), z(km)
num_grid_margin: 5 # number of grid margin
grid_method_1:
lon_min_max: [119.5, 120.5]
lat_min_max: [29.5, 30.5]
grid_method_1: # only read when grid_method: 1; values below describe the same domain as grid_method_0
lon_min_max: [101.8, 104.2] # longitude range in degree
lat_min_max: [23.8, 26.2] # latitude range in degree
n_grid: [100, 100, 30] # number of grid in lon, lat, z

model:
Expand All @@ -39,13 +39,13 @@ model:

topo:
is_consider_topo: False # whether consider topography
topo_file: /path/to/topo.grd # Path to local elevation file. Only valid in topo_type: 1 and 2
topo_file: /path/to/topo.grd # Path to local elevation file. Only valid when is_consider_topo: True
wavelen_factor: 2.5

postproc:
kdensity_coe: 0 # Kdensity_coe is used to rescale the final kernel: kernel -> kernel / pow(density of kernel, Kdensity_coe).
independent_smooth_ani: False # if True, smooth azimuthal anisotropy (Gc/Gs) kernels with sigma_ani / n_inv_grid_ani
smooth_method: 0
smooth_method: 0 # 0: PDE (Gaussian) smoothing; 1: multigrid smoothing
smooth_method_0:
sigma: [0.1, 1] # smoothing lengths [horizontal (degree), vertical (km)]
sigma_ani: [0.15, 1] # same units as sigma; azimuthal anisotropy (Gc/Gs) kernels only, ignored for radial anisotropy (gamma uses sigma)
Expand All @@ -59,12 +59,12 @@ inversion:
model_para_type: 1 # 0 Isotropic, 1 Azimuthal anisotropy, 2 Radial anisotropy
use_alpha_beta_rho: false
rho_scaling: false
vpvs_ratio_range: [1.4, 2.5]
# ------- Inversion parameters --------
niter: 80 # max iterations
vpvs_ratio_range: [1.4, 2.5] # clamp range of vp/vs. Only used when use_alpha_beta_rho: True
# ------- Iteration control -------
niter: 40 # max iterations
min_derr: 0.0015 # minimum error change
# ------- optimization parameters -------
optim_method: 1 # 0: SD (adeptive step length); 1: LBFGS (line search)
optim_method: 1 # 0: SD (adaptive step length); 1: LBFGS (line search)
step_length: 0.02 # starting step length
maxshrink: 0.6 # max step length descent
# ------- Line search for LBFGS -------
Expand Down
16 changes: 8 additions & 8 deletions examples/02_checkerboard_radial_ani/input_params.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,9 +26,9 @@ domain:
grid_method_0:
interval: [0.02, 0.02, 0.2] # interval of lon(degree), lat(degree), z(km)
num_grid_margin: 5 # number of grid margin
grid_method_1:
lon_min_max: [119.5, 120.5]
lat_min_max: [29.5, 30.5]
grid_method_1: # only read when grid_method: 1; values below describe the same domain as grid_method_0
lon_min_max: [101.95, 104.05] # longitude range in degree
lat_min_max: [23.95, 26.05] # latitude range in degree
n_grid: [100, 100, 30] # number of grid in lon, lat, z

model:
Expand All @@ -39,13 +39,13 @@ model:

topo:
is_consider_topo: False # whether consider topography
topo_file: /path/to/topo.grd # Path to local elevation file. Only valid in topo_type: 1 and 2
topo_file: /path/to/topo.grd # Path to local elevation file. Only valid when is_consider_topo: True
wavelen_factor: 2.5

postproc:
kdensity_coe: 0 # Kdensity_coe is used to rescale the final kernel: kernel -> kernel / pow(density of kernel, Kdensity_coe).
independent_smooth_ani: False # if True, smooth azimuthal anisotropy (Gc/Gs) kernels with sigma_ani / n_inv_grid_ani
smooth_method: 0
smooth_method: 0 # 0: PDE (Gaussian) smoothing; 1: multigrid smoothing
smooth_method_0:
sigma: [0.1, 2] # smoothing lengths [horizontal (degree), vertical (km)]
sigma_ani: [0.1, 2] # same units as sigma; azimuthal anisotropy (Gc/Gs) kernels only, ignored for radial anisotropy (gamma uses sigma)
Expand All @@ -59,12 +59,12 @@ inversion:
model_para_type: 2 # 0 Isotropic, 1 Azimuthal anisotropy, 2 Radial anisotropy
use_alpha_beta_rho: false
rho_scaling: false
vpvs_ratio_range: [1.4, 2.5]
# ------- Inversion parameters --------
vpvs_ratio_range: [1.4, 2.5] # clamp range of vp/vs. Only used when use_alpha_beta_rho: True
# ------- Iteration control -------
niter: 40 # max iterations
min_derr: 0.0015 # minimum error change
# ------- optimization parameters -------
optim_method: 1 # 0: SD (adeptive step length); 1: LBFGS (line search)
optim_method: 1 # 0: SD (adaptive step length); 1: LBFGS (line search)
step_length: 0.02 # starting step length
maxshrink: 0.6 # max step length descent
# ------- Line search for LBFGS -------
Expand Down
21 changes: 13 additions & 8 deletions examples/04_hawaii_topo/input_params.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,10 @@ domain:
grid_method_0:
interval: [0.01, 0.01, 0.5] # interval of lon(degree), lat(degree), z(km)
num_grid_margin: 5 # number of grid margin
grid_method_1: # only read when grid_method: 1; values below describe the same domain as grid_method_0
lon_min_max: [-0.52, 0.66] # longitude range in degree (rotated frame, see rotatation.ipynb)
lat_min_max: [-0.47, 0.48] # latitude range in degree (rotated frame)
n_grid: [120, 100, 31] # number of grid in lon, lat, z

model:
# ------- Initial model --------
Expand All @@ -31,16 +35,16 @@ model:

topo:
is_consider_topo: True # whether consider topography
topo_file: hawaii_rotated.nc # Path to local elevation file. Only valid in topo_type: 1 and 2
topo_file: hawaii_rotated.nc # Path to local elevation file. Only valid when is_consider_topo: True
wavelen_factor: 2.5

postproc:
kdensity_coe: 1 # Kdensity_coe is used to rescale the final kernel: kernel -> kernel / pow(density of kernel, Kdensity_coe).
kdensity_coe: 0.0 # Kdensity_coe is used to rescale the final kernel: kernel -> kernel / pow(density of kernel, Kdensity_coe).
independent_smooth_ani: False # if True, smooth azimuthal anisotropy (Gc/Gs) kernels with sigma_ani / n_inv_grid_ani
smooth_method: 1 # 0: PDE (Gaussian) smoothing; 1: multigrid smoothing
smooth_method_0:
sigma: [0.1, 2] # smoothing lengths [horizontal (degree), vertical (km)]
sigma_ani: [0.1, 2] # same units as sigma; azimuthal anisotropy (Gc/Gs) kernels only, ignored for radial anisotropy (gamma uses sigma)
sigma: [0.12, 1.5] # smoothing lengths [horizontal (degree), vertical (km)]
sigma_ani: [0.12, 1.5] # same units as sigma; azimuthal anisotropy (Gc/Gs) kernels only, ignored for radial anisotropy (gamma uses sigma)
smooth_method_1:
n_inv_components: 5
n_inv_grid: [8, 9, 10]
Expand All @@ -49,13 +53,14 @@ postproc:
inversion:
# ------- Inversion parameters --------
model_para_type: 0 # 0 Isotropic, 1 Azimuthal anisotropy, 2 Radial anisotropy
use_alpha_beta_rho: true
rho_scaling: true
# ------- Inversion parameters --------
use_alpha_beta_rho: false
rho_scaling: false
vpvs_ratio_range: [1.4, 2.5] # clamp range of vp/vs. Only used when use_alpha_beta_rho: True
# ------- Iteration control -------
niter: 40 # max iterations
min_derr: 0.0001 # minimum error change
# ------- optimization parameters -------
optim_method: 1 # 0: SD (adeptive step length); 1: LBFGS (line search)
optim_method: 0 # 0: SD (adaptive step length); 1: LBFGS (line search)
step_length: 0.02 # starting step length
maxshrink: 0.6 # max step length descent
# ------- Line search for LBFGS -------
Expand Down
55 changes: 9 additions & 46 deletions examples/04_hawaii_topo/plot_model.ipynb
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55 changes: 11 additions & 44 deletions include/argparser.h
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Expand Up @@ -307,19 +307,14 @@ inline RotateTopoArgs argparse_rotate_topo(int argc, char* argv[]) {
};
}

// Model fields that surfatt_rotate_model is allowed to export. Every entry is a
// scalar field, i.e. invariant under a rotation of the horizontal frame, so only
// the grid coordinates have to be transformed and the values travel unchanged.
inline const std::array<const char*, 7> rotate_model_fields = {
"vs", "vsv", "vsh", "vp", "rho", "zeta", "gamma"
// Model fields written by ModelGrid::write(), plus gamma used by model_iter.h5.
// SURFATT_rotate_model passes scalar fields through unchanged and rotates the
// frame-dependent gc/gs/theta fields together with the grid coordinates.
inline const std::array<const char*, 11> rotate_model_fields = {
"vs", "vp", "rho", "gc", "gs", "g0", "theta",
"vsv", "vsh", "zeta", "gamma"
};

// Fields that are NOT invariant under a frame rotation and must never be exported
// as a plain pass-through: gc/gs are the cos(2*theta)/sin(2*theta) components of
// the azimuthal anisotropy tensor, and theta is the fast-axis azimuth itself (it
// is rotated, but only on the automatic g0/theta columns).
inline const std::array<const char*, 3> rotate_model_blocked_fields = {"gc", "gs", "theta"};

// Comma-separated list of rotate_model_fields, for help text and error messages.
inline std::string rotate_model_fields_str() {
std::string s;
Expand Down Expand Up @@ -359,15 +354,15 @@ inline RotateModelArgs argparse_rotate_model(int argc, char* argv[]) {
" -c clat/clon Centre of rotation (lat/lon)\n\n"
"optional arguments:\n"
" -a angle Rotation angle in degrees (default: 0)\n"
" -k keyname Export only this scalar dataset as the model column\n"
" -k keyname Export only this dataset as the model column\n"
" One of: " << rotate_model_fields_str() << "\n"
" optionally with a model_/grad_ prefix and an _NNN\n"
" iteration suffix, e.g. model_vs_042 in model_iter.h5\n"
" The csv column is named after the bare field, so\n"
" model_vs_042 is written as a column named vs\n"
" Without -k, vs is exported together with whichever\n"
" anisotropy fields the file carries: g0/theta for\n"
" azimuthal, vsv/zeta for radial\n"
" Without -k, every recognised model field present\n"
" in the file is exported. gc/gs/theta are rotated\n"
" together with the coordinate frame.\n"
" -h Print help message\n";
std::exit(0);
}
Expand All @@ -376,34 +371,7 @@ inline RotateModelArgs argparse_rotate_model(int argc, char* argv[]) {
out.outfname = al.require("-o");
if (auto v = al.get("-a")) out.angle = std::stod(*v);
if (auto v = al.get("-c")) out.center = parse_2double(*v);
if (auto v = al.get("-k")) {
const std::string base = rotate_model_base_field(*v);
const auto matches = [&base](const char* k) { return base == k; };
// Reported directly instead of thrown: an uncaught exception under mpirun
// buries the message in an abort trace, and this is a routine user error.
if (std::any_of(rotate_model_blocked_fields.begin(),
rotate_model_blocked_fields.end(), matches)) {
std::cerr << "Error: -k " << *v << " is not supported: \"" << base
<< "\" is not invariant under a rotation of the frame.\n";
if (base == "theta")
std::cerr << "theta is the fast-axis azimuth; it is rotated together with the grid "
"and is\nexported next to g0 when -k is omitted and both are in the "
"file.\n";
else
std::cerr << "gc/gs are the cos(2*theta)/sin(2*theta) components of the azimuthal "
"anisotropy\ntensor; the derived g0/theta pair is exported when -k is "
"omitted.\n";
std::exit(1);
}
if (!std::any_of(rotate_model_fields.begin(), rotate_model_fields.end(), matches)) {
std::cerr << "Error: unknown dataset \"" << *v << "\" for -k.\n"
<< "Allowed fields: " << rotate_model_fields_str() << "\n"
<< "optionally with a model_/grad_ prefix and an _NNN iteration suffix, "
"e.g. model_vs_042\n";
std::exit(1);
}
out.key = *v;
}
if (auto v = al.get("-k")) out.key = *v;
return out;
}

Expand Down Expand Up @@ -432,4 +400,3 @@ inline Tomo2DArgs argparse_tomo2d(int argc, char* argv[]) {
if (auto v = al.get("-m")) out.hmarg = std::stod(*v);
return out;
}

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