colvar::dihedral::dihedral(cvm::atom const &a1,
cvm::atom const &a2,
cvm::atom const &a3,
cvm::atom const &a4)
{
if (cvm::debug())
cvm::log("Initializing dihedral object from atom groups.\n");
function_type = "dihedral";
period = 360.0;
b_periodic = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
b_1site_force = false;
group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2));
group3 = new cvm::atom_group(std::vector<cvm::atom>(1, a3));
group4 = new cvm::atom_group(std::vector<cvm::atom>(1, a4));
atom_groups.push_back(group1);
atom_groups.push_back(group2);
atom_groups.push_back(group3);
atom_groups.push_back(group4);
x.type(colvarvalue::type_scalar);
if (cvm::debug())
cvm::log("Done initializing dihedral object from atom groups.\n");
}
colvar::gyration::gyration()
{
function_type = "gyration";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
x.type(colvarvalue::type_scalar);
}
LoopReductor::LoopReductor(bool _reduce_loops) : Processor((_reduce_loops ? "otawa::LoopReductor" : "otawa::SpanningTreeBuilder"), Version(1, 0, 0)), reduce_loops(_reduce_loops) {
require(COLLECTED_CFG_FEATURE);
invalidate(COLLECTED_CFG_FEATURE);
provide(LOOP_HEADERS_FEATURE);
if (reduce_loops) {
provide(REDUCED_LOOPS_FEATURE);
}
}
colvar::distance_z::distance_z()
{
function_type = "distance_z";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
enable(f_cvc_com_based);
x.type(colvarvalue::type_scalar);
}
colvar::dihedral::dihedral()
{
function_type = "dihedral";
period = 360.0;
b_periodic = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
x.type(colvarvalue::type_scalar);
}
colvar::distance_xy::distance_xy(std::string const &conf)
: distance_z(conf)
{
function_type = "distance_xy";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
enable(f_cvc_com_based);
x.type(colvarvalue::type_scalar);
}
colvar::distance::distance()
: cvc()
{
function_type = "distance";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
enable(f_cvc_com_based);
b_no_PBC = false;
x.type(colvarvalue::type_scalar);
}
colvar::distance_z::distance_z(std::string const &conf)
: cvc(conf)
{
function_type = "distance_z";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
enable(f_cvc_com_based);
x.type(colvarvalue::type_scalar);
// TODO detect PBC from MD engine (in simple cases)
// and then update period in real time
if (period != 0.0)
b_periodic = true;
if ((wrap_center != 0.0) && (period == 0.0)) {
cvm::error("Error: wrapAround was defined in a distanceZ component,"
" but its period has not been set.\n");
return;
}
main = parse_group(conf, "main");
ref1 = parse_group(conf, "ref");
// this group is optional
ref2 = parse_group(conf, "ref2", true);
if (ref2 && ref2->size()) {
cvm::log("Using axis joining the centers of mass of groups \"ref\" and \"ref2\"");
fixed_axis = false;
if (key_lookup(conf, "axis"))
cvm::log("Warning: explicit axis definition will be ignored!");
} else {
if (get_keyval(conf, "axis", axis, cvm::rvector(0.0, 0.0, 1.0))) {
if (axis.norm2() == 0.0) {
cvm::error("Axis vector is zero!");
return;
}
if (axis.norm2() != 1.0) {
axis = axis.unit();
cvm::log("The normalized axis is: "+cvm::to_str(axis)+".\n");
}
}
fixed_axis = true;
}
if (get_keyval(conf, "forceNoPBC", b_no_PBC, false)) {
cvm::log("Computing distance using absolute positions (not minimal-image)");
}
init_total_force_params(conf);
}
colvar::distance::distance(std::string const &conf)
: cvc(conf)
{
function_type = "distance";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
enable(f_cvc_com_based);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
init_total_force_params(conf);
x.type(colvarvalue::type_scalar);
}
colvar::angle::angle(std::string const &conf)
: cvc(conf)
{
function_type = "angle";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
group3 = parse_group(conf, "group3");
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing system force on group 1 only");
}
x.type(colvarvalue::type_scalar);
}
int main(int argc, char **argv)
{
if (argc != 2 && argc != 3) {
print_usage();
goto out;
}
/* compute machine */
if (argc == 2) {
/* local bench configuration */
if (atoi(argv[1]))
compute(atoi(argv[1]), NULL);
/* dsm configuration */
else
compute(0, argv[1]);
/* provider machine */
} else {
provide(argv[1], argv[2]);
}
out:
return 0;
}
void
TraceAnalyzer::recordSideEffects(trace::Call *call)
{
const char *name = call->name();
/* FIXME: If we encode the list of commands that are executed
* immediately (as opposed to those that are compiled into a
* display list) then we could generate a "display-list-X"
* resource just as we do for "texture-X" resources and only
* emit it in the trace if a glCallList(X) is emitted. For
* now, simply punt and include anything within glNewList and
* glEndList in the trim output. This guarantees that display
* lists will work, but does not trim out unused display
* lists. */
if (insideNewEndList != 0) {
provide("state", call->no);
/* Also, any texture bound inside a display list is
* conservatively considered required. */
if (strcmp(name, "glBindTexture") == 0) {
GLuint texture = call->arg(1).toUInt();
linkf("state", "texture-", texture);
}
return;
}
if (trimFlags & TRIM_FLAG_NO_SIDE_EFFECTS) {
if (callHasNoSideEffects(call, name)) {
return;
}
}
if (trimFlags & TRIM_FLAG_TEXTURES) {
if (recordTextureSideEffects(call, name)) {
return;
}
}
if (trimFlags & TRIM_FLAG_SHADERS) {
if (recordShaderSideEffects(call, name)) {
return;
}
}
if (trimFlags & TRIM_FLAG_DRAWING) {
if (recordDrawingSideEffects(call, name)) {
return;
}
}
/* By default, assume this call affects the state somehow. */
resources["state"].insert(call->no);
}
ContextTreeByCFGBuilder::ContextTreeByCFGBuilder(void)
: CFGProcessor("otawa::ContextTreeByCFGBuilder", Version(1, 0, 0)) {
require(DOMINANCE_FEATURE);
require(LOOP_HEADERS_FEATURE);
require(LOOP_INFO_FEATURE);
provide(CONTEXT_TREE_BY_CFG_FEATURE);
}
/* Module init function. */
int
emacs_module_init (struct emacs_runtime *ert)
{
emacs_env *env = ert->get_environment (ert);
#define DEFUN(lsym, csym, amin, amax, doc, data) \
bind_function (env, lsym, \
env->make_function (env, amin, amax, csym, doc, data))
DEFUN ("mod-test-return-t", Fmod_test_return_t, 1, 1, NULL, NULL);
DEFUN ("mod-test-sum", Fmod_test_sum, 2, 2, "Return A + B\n\n(fn a b)", NULL);
DEFUN ("mod-test-signal", Fmod_test_signal, 0, 0, NULL, NULL);
DEFUN ("mod-test-throw", Fmod_test_throw, 0, 0, NULL, NULL);
DEFUN ("mod-test-non-local-exit-funcall", Fmod_test_non_local_exit_funcall,
1, 1, NULL, NULL);
DEFUN ("mod-test-globref-make", Fmod_test_globref_make, 0, 0, NULL, NULL);
DEFUN ("mod-test-string-a-to-b", Fmod_test_string_a_to_b, 1, 1, NULL, NULL);
DEFUN ("mod-test-userptr-make", Fmod_test_userptr_make, 1, 1, NULL, NULL);
DEFUN ("mod-test-userptr-get", Fmod_test_userptr_get, 1, 1, NULL, NULL);
DEFUN ("mod-test-vector-fill", Fmod_test_vector_fill, 2, 2, NULL, NULL);
DEFUN ("mod-test-vector-eq", Fmod_test_vector_eq, 2, 2, NULL, NULL);
#undef DEFUN
provide (env, "mod-test");
return 0;
}
colvar::distance_vec::distance_vec(std::string const &conf)
: distance(conf)
{
function_type = "distance_vec";
provide(f_cvc_com_based);
x.type(colvarvalue::type_3vector);
}
colvar::distance_dir::distance_dir()
: distance()
{
function_type = "distance_dir";
provide(f_cvc_com_based);
x.type(colvarvalue::type_unit3vector);
}
colvar::distance_vec::distance_vec()
: distance()
{
function_type = "distance_vec";
provide(f_cvc_com_based);
x.type(colvarvalue::type_3vector);
}
colvar::gyration::gyration(std::string const &conf)
: cvc(conf)
{
function_type = "gyration";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
atoms = parse_group(conf, "atoms");
if (atoms->b_user_defined_fit) {
cvm::log("WARNING: explicit fitting parameters were provided for atom group \"atoms\".");
} else {
atoms->b_center = true;
atoms->ref_pos.assign(1, cvm::atom_pos(0.0, 0.0, 0.0));
}
x.type(colvarvalue::type_scalar);
}
/**
* Build a new CFG normalizer.
*/
CFGNormalizer::CFGNormalizer(void):
CFGProcessor("otawa::CFGNormalizer", Version(1, 0, 0)),
force(false),
verbose(false)
{
provide(NORMALIZED_CFGS_FEATURE);
require(COLLECTED_CFG_FEATURE);
}
/**
* Constructor.
*/
TextDecoder::TextDecoder(void)
: Processor("otawa::TextDecoder", Version(1, 0, 0)),
follow_paths(false)
{
provide(DECODED_TEXT);
//config(follow_paths_config);
require(FLOW_FACTS_FEATURE);
}
ISPCATBuilder::ISPCATBuilder(void) : CFGProcessor("otawa::ISPCATBuilder", Version(1, 0, 0)) {
require(DOMINANCE_FEATURE);
require(LOOP_HEADERS_FEATURE);
require(LOOP_INFO_FEATURE);
require(COLLECTED_FUNCTIONBLOCKS_FEATURE);
provide(ISP_CAT_FEATURE);
}
EdgeCAT2Builder::EdgeCAT2Builder(void) : CFGProcessor("otawa::EdgeCAT2Builder", Version(1, 0, 0)) {
require(DOMINANCE_FEATURE);
require(LOOP_HEADERS_FEATURE);
require(LOOP_INFO_FEATURE);
require(COLLECTED_LBLOCKS_FEATURE);
require(ICACHE_EDGE_ACS_FEATURE);
require(ICACHE_FIRSTLAST_FEATURE);
provide(ICACHE_EDGE_CATEGORY2_FEATURE);
}
/* Like provide, but with a simply-formatted string, (appending an
* integer to the given string). */
void
TraceAnalyzer::providef(std::string resource,
int resource_no,
trace::CallNo call_no)
{
std::stringstream ss;
ss << resource << resource_no;
provide(ss.str(), call_no);
}
colvar::distance::distance(std::string const &conf)
: cvc(conf)
{
function_type = "distance";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
enable(f_cvc_com_based);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
if (get_keyval(conf, "forceNoPBC", b_no_PBC, false)) {
cvm::log("Computing distance using absolute positions (not minimal-image)");
}
init_total_force_params(conf);
x.type(colvarvalue::type_scalar);
}
colvar::angle::angle(cvm::atom const &a1,
cvm::atom const &a2,
cvm::atom const &a3)
{
function_type = "angle";
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
b_1site_force = false;
group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2));
group3 = new cvm::atom_group(std::vector<cvm::atom>(1, a3));
atom_groups.push_back(group1);
atom_groups.push_back(group2);
atom_groups.push_back(group3);
x.type(colvarvalue::type_scalar);
}
bool
TraceAnalyzer::recordDrawingSideEffects(trace::Call *call, const char *name)
{
/* Handle all rendering operations, (even though only glEnd is
* flagged as a rendering operation we treat everything from
* glBegin through glEnd as a rendering operation). */
if (call->flags & trace::CALL_FLAG_RENDER ||
insideBeginEnd) {
std::set<unsigned> calls;
std::set<unsigned>::iterator c;
provide("framebuffer", call->no);
calls = resolve("render-state");
for (c = calls.begin(); c != calls.end(); c++) {
provide("framebuffer", *c);
}
/* In some cases, rendering has side effects beyond the
* framebuffer update. */
if (renderingHasSideEffect()) {
provide("state", call->no);
for (c = calls.begin(); c != calls.end(); c++) {
provide("state", *c);
}
}
return true;
}
/* Though it's not flagged as a "RENDER" operation, we also want
* to trim swapbuffers calls when trimming drawing operations. */
if (call->flags & trace::CALL_FLAG_SWAP_RENDERTARGET &&
call->flags & trace::CALL_FLAG_END_FRAME) {
return true;
}
/* No known drawing-related side effects. Return false for more analysis. */
return false;
}
colvar::dihedral::dihedral(std::string const &conf)
: cvc(conf)
{
function_type = "dihedral";
period = 360.0;
b_periodic = true;
provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian);
provide(f_cvc_com_based);
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing system force on group 1 only");
}
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
group3 = parse_group(conf, "group3");
group4 = parse_group(conf, "group4");
x.type(colvarvalue::type_scalar);
}
void BinaryFile::do_put(const uint8 *ptr,ulen len)
{
auto src=Range(ptr,len);
while( +src )
{
if( !out ) provide();
ulen delta=Min(src.len,out.len);
(out+=delta).copy( (src+=delta).ptr );
}
}
int
emacs_module_init(struct emacs_runtime *ert)
{
emacs_env *env = ert->get_environment(ert);
#define DEFUN(lsym, csym, amin, amax, doc, data) \
bind_function(env, lsym, env->make_function(env, amin, amax, csym, doc, data))
DEFUN("qrencode-encode", Fqrencode_encode, 2, 2, "Encode string to QRCode", NULL);
#undef DEFUN
provide(env, "qrencode-core");
return 0;
}
int
emacs_module_init(struct emacs_runtime *ert)
{
emacs_env *env = ert->get_environment(ert);
#define DEFUN(lsym, csym, amin, amax, doc, data) \
bind_function (env, lsym, env->make_function(env, amin, amax, csym, doc, data))
DEFUN("mecab-core-new", Fmecab_new, 1, 1, NULL, NULL);
DEFUN("mecab-core-sparse-to-string", Fmecab_sparse_to_string, 3, 3, NULL, NULL);
DEFUN("mecab-core-sparse-to-list", Fmecab_sparse_to_list, 3, 3, NULL, NULL);
#undef DEFUN
provide(env, "mecab-core");
return 0;
}