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If you make the publisher global, you can publish as soon as the message is received in function_callback(). Then the while() loop can be replaced with just ros::spin();

#include "ros/ros.h"
#include <geometry_msgs/Twist.h>
#include "pctx_control/Control.h"
#include "std_msgs/String.h"
#include "pctx_control/pctx.h" 
#include <sstream>

ros::Publisher pub;
pctx_control::Control controlmsg;

void function_callback (const geometry_msgs::Twist &msg) 
{
  controlmsg.ch = 0;
  controlmsg.values[0] = msg.linear.x;
  controlmsg.values[1] = msg.linear.y;
  controlmsg.values[2] = msg.linear.z;
  pub.publish(controlmsg);
  std::cout << "d1" << controlmsg.values[0] << std::endl;
  std::cout << "d2" << controlmsg.values[1] << std::endl;
  std::cout << "d3" << controlmsg.values[2] << std::endl;
}

int main(int argc, char **argv)
{
  ros::init(argc, argv, "my_node");
  ros::NodeHandle n;

  pub = n.advertise<pctx_control::Control>("topic2", 100);

  ros::Subscriber sub = n.subscribe("topic1", 1000, function_callback);

  // Handle ROS callbacks until shutdown
  ros::spin();

  return 0;
}

If you make the publisher global, you can publish as soon as the message is received in function_callback(). Then the while() loop can be replaced with just ros::spin();

#include "ros/ros.h"
#include <geometry_msgs/Twist.h>
#include "pctx_control/Control.h"
#include "std_msgs/String.h"
#include "pctx_control/pctx.h" 
#include <sstream>

ros::Publisher pub;
pctx_control::Control controlmsg;

void function_callback (const geometry_msgs::Twist &msg) 
{
  controlmsg.ch = 0;
  controlmsg.values[0] = msg.linear.x;
controlmsg.values.push_back(msg.linear.x);
 controlmsg.values[1] = msg.linear.y;
controlmsg.values.push_back(msg.linear.y);
 controlmsg.values[2] = msg.linear.z;
controlmsg.values.push_back(msg.linear.z);
  pub.publish(controlmsg);
  std::cout << "d1" << controlmsg.values[0] << std::endl;
  std::cout << "d2" << controlmsg.values[1] << std::endl;
  std::cout << "d3" << controlmsg.values[2] << std::endl;
}

int main(int argc, char **argv)
{
  ros::init(argc, argv, "my_node");
  ros::NodeHandle n;

  pub = n.advertise<pctx_control::Control>("topic2", 100);

  ros::Subscriber sub = n.subscribe("topic1", 1000, function_callback);

  // Handle ROS callbacks until shutdown
  ros::spin();

  return 0;
}

If you make the publisher global, you can publish as soon as the message is received in function_callback(). Then the while() loop can be replaced with just ros::spin();

#include "ros/ros.h"
#include <geometry_msgs/Twist.h>
#include "pctx_control/Control.h"
#include "std_msgs/String.h"
#include "pctx_control/pctx.h" 
#include <sstream>

ros::Publisher pub;
pctx_control::Control controlmsg;

void function_callback (const geometry_msgs::Twist &msg) 
{
  controlmsg.ch = 0;
  controlmsg.values.push_back(msg.linear.x);
controlmsg.values.resize(3);
 controlmsg.values.push_back(msg.linear.y);
controlmsg.values[0] = msg.linear.x;
 controlmsg.values.push_back(msg.linear.z);
controlmsg.values[1] = msg.linear.y;
  controlmsg.values[2] = msg.linear.z;
  pub.publish(controlmsg);
  std::cout << "d1" << controlmsg.values[0] << std::endl;
  std::cout << "d2" << controlmsg.values[1] << std::endl;
  std::cout << "d3" << controlmsg.values[2] << std::endl;
}

int main(int argc, char **argv)
{
  ros::init(argc, argv, "my_node");
  ros::NodeHandle n;

  pub = n.advertise<pctx_control::Control>("topic2", 100);

  ros::Subscriber sub = n.subscribe("topic1", 1000, function_callback);

  // Handle ROS callbacks until shutdown
  ros::spin();

  return 0;
}

Edit: Changed vector indexing to push_back()push_back()
Edit: Changed vector indexing back to brackets, and reinitialize with resize() every iteration per comment from @dornhege