Minor code format wih [email protected] (#73)

Author: pramodk

coreneuron/coreneuron.h

@@ -30,7 +30,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
  * Includes all headers required to communicate and run all methods
  * described in CoreNeuron, neurox, and mod2c C-generated mechanisms
  * functions.
-**/
+ **/
 
 #ifndef CORENEURON_H
 #define CORENEURON_H

coreneuron/nrniv/multisend.cpp

@@ -42,7 +42,6 @@ of spikes sent is equal to the number of spikes sent.
 // which has the greatest amount of overlap between computation
 // and communication.
 
-
 int use_multisend_;
 int use_phase2_;
 int n_multisend_interval = 2;
@@ -104,7 +103,6 @@ class Multisend_ReceiveBuffer {
     Phase2Buffer* phase2_buffer_;
 };
 
-
 #define MULTISEND_INTERVAL 2
 static Multisend_ReceiveBuffer* multisend_receive_buffer[MULTISEND_INTERVAL];
 static int current_rbuf, next_rbuf;
@@ -468,4 +466,4 @@ void nrn_multisend_setup() {
 #endif
 }
 
-#endif //NRN_MULTISEND
+#endif  // NRN_MULTISEND

coreneuron/nrniv/multisend_setup.cpp

@@ -703,4 +703,4 @@ static int setup_target_lists(int use_phase2, int** r_return) {
     return sz;
 }
 
-#endif //NRN_MULTISEND
+#endif  // NRN_MULTISEND

coreneuron/nrniv/output_spikes.cpp

@@ -29,7 +29,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include <iostream>
 #include <sstream>
 #include <string.h>
-#include <stdexcept> // std::lenght_error
+#include <stdexcept>  // std::lenght_error
 #include <vector>
 #include "coreneuron/nrnconf.h"
 #include "coreneuron/nrniv/nrniv_decl.h"
@@ -47,10 +47,10 @@ static MUTDEC
     void
     mk_spikevec_buffer(int sz) {
     try {
-      spikevec_time.reserve(sz);
-      spikevec_gid.reserve(sz);
+        spikevec_time.reserve(sz);
+        spikevec_gid.reserve(sz);
     } catch (const std::length_error& le) {
-      std::cerr << "Lenght error" << le.what() << std::endl;
+        std::cerr << "Lenght error" << le.what() << std::endl;
     }
     MUTCONSTRUCT(1);
 }
@@ -74,7 +74,7 @@ void output_spikes_parallel(const char* outpath) {
     std::string fname = ss.str();
 
     // remove if file already exist
-    if(nrnmpi_myid == 0) {
+    if (nrnmpi_myid == 0) {
         remove(fname.c_str());
     }
     nrnmpi_barrier();
@@ -83,9 +83,9 @@ void output_spikes_parallel(const char* outpath) {
     const int SPIKE_RECORD_LEN = 64;
     unsigned num_spikes = spikevec_gid.size();
     unsigned num_bytes = (sizeof(char) * num_spikes * SPIKE_RECORD_LEN);
-    char *spike_data = (char*) malloc(num_bytes);
+    char* spike_data = (char*)malloc(num_bytes);
 
-    if(spike_data == NULL) {
+    if (spike_data == NULL) {
         printf("Error while writing spikes due to memory allocation\n");
         return;
     }
@@ -95,7 +95,7 @@ void output_spikes_parallel(const char* outpath) {
 
     // populate buffer with all spike entries
     char spike_entry[SPIKE_RECORD_LEN];
-    for(unsigned i = 0; i < num_spikes; i++) {
+    for (unsigned i = 0; i < num_spikes; i++) {
         snprintf(spike_entry, 64, "%.8g\t%d\n", spikevec_time[i], spikevec_gid[i]);
         strcat(spike_data, spike_entry);
     }
@@ -113,14 +113,15 @@ void output_spikes_parallel(const char* outpath) {
     MPI_Status status;
 
     // ibm mpi (bg-q) expects char* instead of const char* (even though it's standard)
-    int op_status = MPI_File_open(MPI_COMM_WORLD, (char*) fname.c_str(), MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL, &fh);
-    if(op_status != MPI_SUCCESS && nrnmpi_myid == 0) {
+    int op_status = MPI_File_open(MPI_COMM_WORLD, (char*)fname.c_str(),
+                                  MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL, &fh);
+    if (op_status != MPI_SUCCESS && nrnmpi_myid == 0) {
         std::cerr << "Error while opening spike output file " << fname << std::endl;
         abort();
     }
 
     op_status = MPI_File_write_at_all(fh, offset, spike_data, num_chars, MPI_BYTE, &status);
-    if(op_status != MPI_SUCCESS && nrnmpi_myid == 0) {
+    if (op_status != MPI_SUCCESS && nrnmpi_myid == 0) {
         std::cerr << "Error while writing spike output " << std::endl;
         abort();
     }
@@ -152,7 +153,7 @@ void output_spikes_serial(const char* outpath) {
 
 void output_spikes(const char* outpath) {
 #if NRNMPI
-    if(nrnmpi_initialized()) {
+    if (nrnmpi_initialized()) {
         output_spikes_parallel(outpath);
     } else {
         output_spikes_serial(outpath);
@@ -162,7 +163,6 @@ void output_spikes(const char* outpath) {
 #endif
 }
 
-
 void validation(std::vector<std::pair<double, int> >& res) {
     for (unsigned i = 0; i < spikevec_gid.size(); ++i)
         if (spikevec_gid[i] > -1)

coreneuron/nrniv/patternstim.cpp

@@ -85,7 +85,7 @@ void nrn_mkPatternStim(const char* fname) {
     }
 
     // if there is empty thread then return, don't need patternstim
-    if(nrn_threads == NULL || nrn_threads->ncell == 0) {
+    if (nrn_threads == NULL || nrn_threads->ncell == 0) {
         return;
     }
 
@@ -120,7 +120,7 @@ void nrn_mkPatternStim(const char* fname) {
 // comparator to sort spikes based on time
 typedef std::pair<double, int> spike_type;
 static bool spike_comparator(const spike_type& l, const spike_type& r) {
-        return l.first < r.first;
+    return l.first < r.first;
 }
 
 size_t read_raster_file(const char* fname, double** tvec, int** gidvec) {
@@ -146,15 +146,15 @@ size_t read_raster_file(const char* fname, double** tvec, int** gidvec) {
     // pattern.mod expects sorted spike raster (this is to avoid
     // injecting all events at the begining of the simulation).
     // sort spikes according to time
-    std::sort(spikes.begin(), spikes.end(),  spike_comparator);
+    std::sort(spikes.begin(), spikes.end(), spike_comparator);
 
     // fill gid and time vectors
     *tvec = (double*)emalloc(spikes.size() * sizeof(double));
     *gidvec = (int*)emalloc(spikes.size() * sizeof(int));
 
-    for(size_t i = 0; i < spikes.size(); i++) {
-         (*tvec)[i] = spikes[i].first;
-         (*gidvec)[i] = spikes[i].second;
+    for (size_t i = 0; i < spikes.size(); i++) {
+        (*tvec)[i] = spikes[i].first;
+        (*gidvec)[i] = spikes[i].second;
     }
 
     return spikes.size();
@@ -171,7 +171,7 @@ Point_process* nrn_artcell_instantiate(const char* mechname) {
     int type = nrn_get_mechtype(mechname);
     NrnThread* nt = nrn_threads + 0;
 
-    //printf("nrn_artcell_instantiate %s type=%d\n", mechname, type);
+    // printf("nrn_artcell_instantiate %s type=%d\n", mechname, type);
 
     // see nrn_setup.cpp:read_phase2 for how it creates NrnThreadMembList instances.
     // create and append to nt.tml

coreneuron/nrnoc/solve_core.c

@@ -32,7 +32,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 
 int use_solve_interleave;
 
-static void triang(NrnThread *), bksub(NrnThread *);
+static void triang(NrnThread*), bksub(NrnThread*);
 
 /* solve the matrix equation */
 void nrn_solve_minimal(NrnThread* _nt) {
@@ -63,9 +63,12 @@ static void triang(NrnThread* _nt) {
 #endif
 
 /** @todo: just for benchmarking, otherwise produces wrong results */
-#pragma acc parallel loop seq present(                                                  \
-    vec_a[0 : i3], vec_b[0 : i3], vec_d[0 : i3], vec_rhs[0 : i3], parent_index[0 : i3]) \
-                                                     async(stream_id) if (_nt->compute_gpu)
+// clang-format off
+    #pragma acc parallel loop seq present(      \
+        vec_a[0:i3], vec_b[0:i3], vec_d[0:i3],  \
+        vec_rhs[0:i3], parent_index[0:i3])      \
+        async(stream_id) if (_nt->compute_gpu)
+    // clang-format on
     for (i = i3 - 1; i >= i2; --i) {
         p = vec_a[i] / vec_d[i];
         vec_d[parent_index[i]] -= p * vec_b[i];

coreneuron/scopmath_core/dimplic.c

@@ -10,7 +10,7 @@
  *  time.
  *  \todo: eulerfun/difun are legacy macros and can be replaced with
  *         actual steer function for euler/derivimplicit methods.
-*/
+ */
 
 #include "coreneuron/mech/cfile/scoplib.h"
 #include "coreneuron/mech/mod2c_core_thread.h"
@@ -44,16 +44,15 @@ int nrn_kinetic_steer(int fun, SparseObj* so, double* rhs, _threadargsproto_) {
 // derived from nrn/src/scopmath/euler.c
 // updated for aos/soa layout index
 int euler_thread(int neqn, int* var, int* der, DIFUN fun, _threadargsproto_) {
-
     double dt = _nt->_dt;
     int i;
 
     /* calculate the derivatives */
-     eulerfun(fun);
+    eulerfun(fun);
 
     /* update dependent variables */
     for (i = 0; i < neqn; i++)
-        _p[var[i]*_STRIDE] += dt * (_p[der[i]*_STRIDE]);
+        _p[var[i] * _STRIDE] += dt * (_p[der[i] * _STRIDE]);
 
     return 0;
 }