From dd4e182bc818974b3ad529422e631aa6a0764f2f Mon Sep 17 00:00:00 2001
From: Samo Penic <samo.penic@fe.uni-lj.si>
Date: Tue, 05 Jul 2016 10:18:24 +0000
Subject: [PATCH] Merge branch 'nirgov' of bitbucket.org:samop/trisurf-ng into nirgov
---
src/snapshot.c | 65 ++++++++++++++++++--------------
1 files changed, 36 insertions(+), 29 deletions(-)
diff --git a/src/snapshot.c b/src/snapshot.c
index 9dc23a9..fbb6d4b 100644
--- a/src/snapshot.c
+++ b/src/snapshot.c
@@ -1,3 +1,5 @@
+/* vim: set ts=4 sts=4 sw=4 noet : */
+/* vim: set ts=4 sts=4 sw=4 noet : */
#include<stdio.h>
#include<general.h>
#include<snapshot.h>
@@ -30,6 +32,8 @@
xml_trisurf_tria_neigh(data,vesicle->tlist);
xml_trisurf_vtx_neigh(data,vesicle->vlist);
xml_trisurf_vtx_tristar(data,vesicle->vlist);
+ xml_trisurf_nucleus(data,vesicle);
+ xml_trisurf_constvolarea(data,V0,A0);
#ifdef COMPRESSION
char *compressed;
ts_uint nbytes=ts_compress_string64(data->string, data->beg-1, &compressed); //suppress null character at the end with by substracting 1
@@ -55,7 +59,7 @@
fprintf(fh, "<trisurfversion>Trisurf (commit %s), compiled on %s %s</trisurfversion>\n",TS_VERSION, __DATE__, __TIME__);
fprintf(fh, "<dumpdate>%s</dumpdate>\n", c_time_string);
- fprintf(fh, "<tape>\n");
+ fprintf(fh, "<tape>");
fprintf(fh,"%s",tapetxt);
fprintf(fh, "</tape>\n");
if(vesicle->poly_list!=NULL){
@@ -122,7 +126,18 @@
return TS_SUCCESS;
}
+ts_bool xml_trisurf_nucleus(ts_string *data, ts_vesicle* vesicle){
+ if(vesicle->R_nucleus>0.0 || (vesicle->R_nucleusX>0.0 && vesicle->R_nucleusY>0.0 && vesicle->R_nucleusZ>0.0)){
+ ts_sprintf(data,"<nucleus>%.17e %.17e %.17e</nucleus>",vesicle->nucleus_center[0], vesicle->nucleus_center[1], vesicle->nucleus_center[2]);
+ }
+ return TS_SUCCESS;
+}
+ts_bool xml_trisurf_constvolarea(ts_string *data, ts_double volume, ts_double area){
+ ts_sprintf(data,"<constant_volume>%.17e</constant_volume>",volume);
+ ts_sprintf(data,"<constant_area>%.17e</constant_area>",area);
+ return TS_SUCCESS;
+}
/* UTILITIES */
@@ -169,10 +184,7 @@
static int mod_table[] = {0, 2, 1};
-char *base64_encode(const unsigned char *data,
- size_t input_length,
- size_t *output_length) {
-
+char *base64_encode(const unsigned char *data, size_t input_length, size_t *output_length) {
*output_length = 4 * ((input_length + 2) / 3);
int i,j;
char *encoded_data = malloc(*output_length);
@@ -180,29 +192,25 @@
for (i = 0, j = 0; i < input_length;) {
- uint32_t octet_a = i < input_length ? (unsigned char)data[i++] : 0;
- uint32_t octet_b = i < input_length ? (unsigned char)data[i++] : 0;
- uint32_t octet_c = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t octet_a = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t octet_b = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t octet_c = i < input_length ? (unsigned char)data[i++] : 0;
+ uint32_t triple = (octet_a << 0x10) + (octet_b << 0x08) + octet_c;
- uint32_t triple = (octet_a << 0x10) + (octet_b << 0x08) + octet_c;
-
- encoded_data[j++] = encoding_table[(triple >> 3 * 6) & 0x3F];
- encoded_data[j++] = encoding_table[(triple >> 2 * 6) & 0x3F];
- encoded_data[j++] = encoding_table[(triple >> 1 * 6) & 0x3F];
- encoded_data[j++] = encoding_table[(triple >> 0 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 3 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 2 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 1 * 6) & 0x3F];
+ encoded_data[j++] = encoding_table[(triple >> 0 * 6) & 0x3F];
}
for (i = 0; i < mod_table[input_length % 3]; i++)
- encoded_data[*output_length - 1 - i] = '=';
+ encoded_data[*output_length - 1 - i] = '=';
return encoded_data;
}
-unsigned char *base64_decode(const char *data,
- size_t input_length,
- size_t *output_length) {
-
+unsigned char *base64_decode(const char *data, size_t input_length, size_t *output_length) {
int i,j;
if (decoding_table == NULL) build_decoding_table();
@@ -216,20 +224,19 @@
if (decoded_data == NULL) return NULL;
for (i = 0, j = 0; i < input_length;) {
+ uint32_t sextet_a = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
+ uint32_t sextet_b = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
+ uint32_t sextet_c = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
+ uint32_t sextet_d = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_a = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_b = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_c = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
- uint32_t sextet_d = data[i] == '=' ? 0 & i++ : decoding_table[(int)data[i++]];
-
- uint32_t triple = (sextet_a << 3 * 6)
+ uint32_t triple = (sextet_a << 3 * 6)
+ (sextet_b << 2 * 6)
+ (sextet_c << 1 * 6)
+ (sextet_d << 0 * 6);
- if (j < *output_length) decoded_data[j++] = (triple >> 2 * 8) & 0xFF;
- if (j < *output_length) decoded_data[j++] = (triple >> 1 * 8) & 0xFF;
- if (j < *output_length) decoded_data[j++] = (triple >> 0 * 8) & 0xFF;
+ if (j < *output_length) decoded_data[j++] = (triple >> 2 * 8) & 0xFF;
+ if (j < *output_length) decoded_data[j++] = (triple >> 1 * 8) & 0xFF;
+ if (j < *output_length) decoded_data[j++] = (triple >> 0 * 8) & 0xFF;
}
if(decoding_table !=NULL) free(decoding_table);
return decoded_data;
@@ -241,7 +248,7 @@
decoding_table = malloc(256);
int i;
for (i = 0; i < 64; i++)
- decoding_table[(unsigned char) encoding_table[i]] = i;
+ decoding_table[(unsigned char) encoding_table[i]] = i;
}
--
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